A fixed-target platform for serial femtosecond crystallography in a hydrated environment.

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering

A rare and exclusive endoperoxide photoproduct derived from thiacalix[4]arene crown-shaped derivative bearing 9,10-substituted anthracene moiety

A rare and exclusive endoperoxide photoproduct was quantitatively obtained from a thiacalix[4]arene crown-shaped derivative upon irradiation at λ=365 nm; the structure was unambiguously confirmed by 1H/13C NMR spectroscopy and X-ray crystallography. The prerequisites for the formation of the endoperoxide photoproduct have also been discussed. Furthermore, the photochemical reaction rate could be greatly enhanced in the presence of the thiacalix[4]arene platform because it served as a host to capture oxygen

Hexabenzo[4.4.4]propellane: A Helical Molecular Platform for the Construction of Electroactive Materials

Helical hexabenzo[4.4.4]propellane (a relative of hexaphenylethane) and its derivatives are synthesized and their structures are established by X-ray crystallography. Isolation and X-ray crystallographic characterization of a robust trication-radical salt of hexamethoxypropellane derivative confirms that its framework is stable toward oxidative (aliphatic) C−C bond cleavage. It is also demonstrated that propellane can be easily brominated at the 4,4‘-positions of the biphenyl linkages for its usage as a molecular platform for the preparation of electroactive materials

Archiving and disseminating integrative structure models.

Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format

A posteriori metadata from automated provenance tracking: Integration of AiiDA and TCOD

In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Here the implementation of a protocol is presented to tag crystal structures with their computed properties, without the need of human intervention to curate the data. This protocol leverages the capabilities of AiiDA, an open-source platform to manage and automate scientific computational workflows, and TCOD, an open-access database storing computed materials properties using a well-defined and exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD database is automated. All relevant metadata are extracted from the full provenance information that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also enables reproducibility of scientific data in the field of computational materials science. As a proof of concept, the AiiDA-TCOD interface is used to deposit 170 theoretical structures together with their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes

Building a Disciplinary, World-Wide Data Infrastructure

Sharing scientific data, with the objective of making it fully discoverable, accessible, assessable, intelligible, usable, and interoperable, requires work at the disciplinary level to define in particular how the data should be formatted and described. Each discipline has its own organization and history as a starting point, and this paper explores the way a range of disciplines, namely materials science, crystallography, astronomy, earth sciences, humanities and linguistics get organized at the international level to tackle this question. In each case, the disciplinary culture with respect to data sharing, science drivers, organization and lessons learnt are briefly described, as well as the elements of the specific data infrastructure which are or could be shared with others. Commonalities and differences are assessed. Common key elements for success are identified: data sharing should be science driven; defining the disciplinary part of the interdisciplinary standards is mandatory but challenging; sharing of applications should accompany data sharing. Incentives such as journal and funding agency requirements are also similar. For all, it also appears that social aspects are more challenging than technological ones. Governance is more diverse, and linked to the discipline organization. CODATA, the RDA and the WDS can facilitate the establishment of disciplinary interoperability frameworks. Being problem-driven is also a key factor of success for building bridges to enable interdisciplinary research.Comment: Proceedings of the session "Building a disciplinary, world-wide data infrastructure" of SciDataCon 2016, held in Denver, CO, USA, 12-14 September 2016, to be published in ICSU CODATA Data Science Journal in 201

Computing and teaching microsymposia at ECM [European Crystallographic Meeting 20, Krakow, August 2001]

Microsymposia on the contemporary topic of Computing and Teaching Some key issues regarding different models for delivery of the curriculum, the pace of introducing the new technologies, the role of government in delivering mass education and the pressures on institutions in responding to the novel methods of education were raised during the talks

Terphenyl Crowns: a New Family of Receptors Containing Ethereal Canopies that Direct Potassium Cation onto Benzenoid Platforms for Cation–π Interactions

We have synthesized three simple and versatile terphenyl crowns (TC) receptors containing ethereal canopies that direct a potassium cation for efficient cation–π interactions as established by 1H NMR spectroscopy and by isolation and X-ray crystallography of their K+ salts

A suite of software for processing MicroED data of extremely small protein crystals.

Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. This ad hoc solution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License