64 research outputs found
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
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for
predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical
connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection
of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access
basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do
not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the
SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable
image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.),
the previously published cif_molecule program is used to get such image in many cases. The program package
Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those
produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a
computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be
improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical
structures and the purpose of this article is to announce the existence of this work to the chemical community as well
as to spread the use of its results.The authors are grateful to the Junta de Andalucía (Research Group FQM-195)
for financial support of the publication costs of this article
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database
Computer descriptions of chemical molecular connectivity are necessary for searching chemical databases and for
predicting chemical properties from molecular structure. In this article, the ongoing work to describe the chemical
connectivity of entries contained in the Crystallography Open Database (COD) in SMILES format is reported. This collection
of SMILES is publicly available for chemical (substructure) search or for any other purpose on an open-access
basis, as is the COD itself. The conventions that have been followed for the representation of compounds that do
not fit into the valence bond theory are outlined for the most frequently found cases. The procedure for getting the
SMILES out of the CIF files starts with checking whether the atoms in the asymmetric unit are a chemically acceptable
image of the compound. When they are not (molecule in a symmetry element, disorder, polymeric species,etc.),
the previously published cif_molecule program is used to get such image in many cases. The program package
Open Babel is then applied to get SMILES strings from the CIF files (either those directly taken from the COD or those
produced by cif_molecule when applicable). The results are then checked and/or fixed by a human editor, in a
computer-aided task that at present still consumes a great deal of human time. Even if the procedure still needs to be
improved to make it more automatic (and hence faster), it has already yielded more than 160,000 curated chemical
structures and the purpose of this article is to announce the existence of this work to the chemical community as well
as to spread the use of its results.The authors are grateful to the Junta de Andalucía (Research Group FQM-195)
for financial support of the publication costs of this article
Light-Responsive Oligothiophenes Incorporating Photochromic Torsional Switches (PTS)
We present a quaterthiophene and sexithiophene that can reversibly change their effective π-conjugation length via photoexcitation. The reported compounds make use of light-responsive molecular actuators consisting of an azobenzene attached to a bithiophene unit by both direct and linker-assisted bonding. Upon exposure to 350 nm light the azobenzene undergoes trans -to- cis isomerization mechanically inducing the oligothiophene to assume a planar conformations (extended π-conjugation). Exposure to 254 nm wavelenght promotes azobenzene cis -to- trans isomerization, forcing the thiophenic backbones to twist out of planarity (confined π-conjugation). Twisted conformations are also reached by cis -to- trans thermal relaxation with rate that increases proportionally with the conjugation length of the oligothiophene moiety. The molecular conformations of quaterthiophene and sexithiophene were characterized using steady-state UV-vis, X-ray crystallography and quantum-chemical modelling. Finally, we tested the proposed light-responsive oligothiophenes into field-effect transistors to probe the photo-induced tuning of their electronic properties
Crystallography Open Database – an open-access collection of crystal structures
The Crystallography Open Database (COD) is an ongoing initiative by crystallographers to gather all published inorganic, metal–organic and small organic molecule structures in one database, providing a straightforward search and retrieval interface. The COD adopts an open-access model for its >80 000 structure files
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration
Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge
Crystallographic Education in the 21st Century
There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described
OPTIMADE, an API for exchanging materials data
The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification
OPTIMADE, an API for exchanging materials data
: The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification
OPTIMADE, an API for exchanging materials data.
The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification
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