Ring Rotation in Ferrocene and Ferrocene-containing Polymers

Ferrocene is an organometallic molecular sandwich complex with an iron atom coordinated between two cyclopentadienyl rings. The reorientation of these rings in a process of rotational jump diffusion between multiple equilibrium sites on a circle is investigated using quasielastic neutron time of flight and backscattering spectroscopy experiments. Existing results on the ring rotation in bulk, crystalline ferrocene are extended, and the study is widened to oxidized ferrocenium cations in the triiodide complex FcI3, and to ferrocene containing polymers like poly(vinylferrocene) PVFc. Emphasis is put on a robust data analysis of neutron scattering data, including corrections for multiple scattering and simultaneous analysis of many data sets taken on different spectrometers. It is shown that the 5-fold rotational jump diffusion model needs to be extended to a non-equivalent sites model to account for rotational disorder in the monoclinic room temperature phase of ferrocene which is metastable down to 164K. In the triclinic phase below 164K, the combination of time of flight and backscattering spectroscopy enables to separate two dynamical processes due to crystallographically different molecules in the unit cell. In the triiodide complex of ferrocenium cations, FcI3, the barrier to rotation is found to be significantly lower than in bulk ferrocene. Moreover, a hitherto unknown phase transition is found at 85K which causes a discontinuity in the temperature dependence of the correlation time of the ring rotation in FcI3, very similar to the triclinic-monoclinic transition in ferrocene. The ring rotation above 85K is closer to continuous rotation due to its low barrier, while 5-fold jumps are favored below 85K. In the polymer PVFc, where ferrocene units are laterally attached to a polymer chain, it is shown that the ring rotation is still active, but the correlation times are broadly distributed. The neutron scattering data can be described very well by a rotation rate distribution model over the large temperature range from 80K to 350K. The average activation energy of the motion is 9.61(2)kJ/mol, with a distribution having circa one third of this value as second moment. Moreover, a vibrational study has been performed on ferrocene, FcI3, and various ferrocene containing polymers. It turns out that the vibrational fingerprint modes of the molecule are mildly affected when the ferrocene unit is laterally attached to a polymer chain, but more severely if it is incorporated into the polymer backbone. Finally, measurements under external magnetic fields did not reveal any field dependence of the ring rotation dynamics in oxidized PVFc, where the oxidation leads to magnetic moments on the ferrocene units. Even though unrelated to the main topic of ring rotation, these experiments nicely demonstrated inelastic magnetic neutron scattering on Zeeman split levels of the electronic ground state, and high resolution measurements allowed to directly observe nuclear hyperfine splitting in external magnetic fields

The realization of autonomous, aircraft-based, real-time aerosol mass spectrometry in the upper troposphere and lower stratosphere

We report on the developments that enabled the field deployment of a fully automated aerosol mass spectrometer, especially designed for high-altitude measurements on unpressurized aircraft. The merits of the two main categories of real-time aerosol mass spectrometry, i.e. (a) single-particle laser desorption and ionization and (b) continuous thermal desorption and electron impact ionization of aerosols, have been integrated into one compact apparatus with the aim to perform in situ real-time analysis of aerosol chemical composition. The demonstrated instrument, named the ERICA (European Research Council Instrument for Chemical composition of Aerosols), operated successfully aboard the high-altitude research aircraft M-55 Geophysica at altitudes up to 20 km while being exposed to ambient conditions of very low atmospheric pressure and temperature. A primary goal of those field deployments was the in situ study of the Asian tropopause aerosol layer (ATAL). During 11 research flights, the instrument operated for more than 49 h and collected chemical composition information of more than 150 000 single particles combined with quantitative chemical composition analysis of aerosol particle ensembles. This paper presents in detail the technical characteristics of the main constituent parts of the instrument, as well as the design considerations for its integration into the aircraft and its autonomous operation in the upper troposphere and lower stratosphere (UTLS). Additionally, system performance data from the first field deployments of the instrument are presented and discussed, together with exemplary mass spectrometry data collected during those flights

ExtremeEarth meets satellite data from space

Bringing together a number of cutting-edge technologies that range from storing extremely large volumesof data all the way to developing scalable machine learning and deep learning algorithms in a distributed manner, and having them operate over the same infrastructure poses unprecedentedchallenges. One of these challenges is the integration of European Space Agency (ESA)s Thematic Exploitation Platforms (TEPs) and data information access service platforms with a data platform, namely Hopsworks, that enables scalable data processing, machine learning, and deep learning on Copernicus data, and development of very large training datasets for deep learning architectures targeting the classification of Sentinel images. In this paper, we present the software architecture of ExtremeEarth that aims at the development of scalable deep learning and geospatial analytics techniques for processing and analyzing petabytes of Copernicus data. The ExtremeEarth software infrastructure seamlessly integrates existing and novel software platforms and tools for storing, accessing, processing, analyzing, and visualizing large amounts of Copernicus data. New techniques in the areas of remote sensing and artificial intelligence with an emphasis on deep learning are developed. These techniques and corresponding software presented in thispaper are to be integrated with and used in two ESA TEPs, namely Polar and Food Security TEPs. Furthermore, we presentthe integration of Hopsworks with the Polar and Food Securityuse cases and the flow of events for the products offered through the TEPs

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Ring Rotation in Ferrocene and Ferrocene-containing Polymers

Ferrocene is an organometallic molecular sandwich complex with an iron atom coordinated between two cyclopentadienyl rings. The reorientation of these rings in a process of rotational jump diffusion between multiple equilibrium sites on a circle is investigated using quasielastic neutron time of flight and backscattering spectroscopy experiments. Existing results on the ring rotation in bulk, crystalline ferrocene are extended, and the study is widened to oxidized ferrocenium cations in the triiodide complex FcI3, and to ferrocene containing polymers like poly(vinylferrocene) PVFc. Emphasis is put on a robust data analysis of neutron scattering data, including corrections for multiple scattering and simultaneous analysis of many data sets taken on different spectrometers. It is shown that the 5-fold rotational jump diffusion model needs to be extended to a non-equivalent sites model to account for rotational disorder in the monoclinic room temperature phase of ferrocene which is metastable down to 164K. In the triclinic phase below 164K, the combination of time of flight and backscattering spectroscopy enables to separate two dynamical processes due to crystallographically different molecules in the unit cell. In the triiodide complex of ferrocenium cations, FcI3, the barrier to rotation is found to be significantly lower than in bulk ferrocene. Moreover, a hitherto unknown phase transition is found at 85K which causes a discontinuity in the temperature dependence of the correlation time of the ring rotation in FcI3, very similar to the triclinic-monoclinic transition in ferrocene. The ring rotation above 85K is closer to continuous rotation due to its low barrier, while 5-fold jumps are favored below 85K. In the polymer PVFc, where ferrocene units are laterally attached to a polymer chain, it is shown that the ring rotation is still active, but the correlation times are broadly distributed. The neutron scattering data can be described very well by a rotation rate distribution model over the large temperature range from 80K to 350K. The average activation energy of the motion is 9.61(2)kJ/mol, with a distribution having circa one third of this value as second moment. Moreover, a vibrational study has been performed on ferrocene, FcI3, and various ferrocene containing polymers. It turns out that the vibrational fingerprint modes of the molecule are mildly affected when the ferrocene unit is laterally attached to a polymer chain, but more severely if it is incorporated into the polymer backbone. Finally, measurements under external magnetic fields did not reveal any field dependence of the ring rotation dynamics in oxidized PVFc, where the oxidation leads to magnetic moments on the ferrocene units. Even though unrelated to the main topic of ring rotation, these experiments nicely demonstrated inelastic magnetic neutron scattering on Zeeman split levels of the electronic ground state, and high resolution measurements allowed to directly observe nuclear hyperfine splitting in external magnetic fields

A flexible high speed pulse chopper system for an inverted neutron time-of-flight option on backscattering spectrometers

We present the design and simulation of a high resolution inverted time-of-flight option for a neutron spectrometer with crystal analysers in backscattering, with specific reference to the IN16B spectrometer at the Institut Laue-Langevin, Grenoble. While the conventional configuration with Si 111 crystals provides sub-μeV resolution in an energy range limited to ±30 μeV, the novel BATS option (BATS: Backscattering and Time-of-flight Spectrometer) extends the energy window to 340 μeV with only a slightly increased resolution of 1.2 μeV. Moreover, the observation window can be shifted to inelastic energy transfers. To bring this about, a novel fast chopper system with disks of large diameter and complex slit pattern is used, offering high flexibility in resolution and repetition rate. The chopper system consists out of two counter rotating disk chopper pairs. It provides 7 different pulse lengths, three pulse repetition rates up to 237 Hz and can operate with Si 111 or Si 311 crystal analysers. The latter option is a unique feature which covers a Q-range up to 3.7 Å−1 with a resolution of 6.8 μeV. Extensive ray-tracing simulations have been used to validate the design of the pulse chopper system, set limits on the sample size, and assess the achievable energy resolutions of the different chopper configurations

Signature of functional enzyme dynamics in quasielastic neutron scattering spectra: The case of phosphoglycerate kinase

International audienceWe present an analysis of high-resolution quasi-elastic neutron scattering spectra of phosphoglycerate kinase which elucidates the influence of the enzymatic activity on the dynamics of the protein. We show that in the active state the inter-domain motions are amplified and the intra-domain asymptotic power-law relaxation ∝t−α is accelerated, with a reduced coefficient α. Employing an energy landscape picture of protein dynamics, this observation can be translated into a widening of the distribution of energy barriers separating conformational substates of the protein

Multiscale relaxation dynamics and diffusion of myelin basic protein in solution studied by quasielastic neutron scattering

International audienc