Managing the Computational Chemistry Big Data Problem: The ioChem-BD Platform

Abstract

We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

Single Electron Transfer Steps in Water Oxidation Catalysis. Redefining the Mechanistic Scenario

“…A dataset collection of computational results is available in the iochem-db database. 50 This material is available free of charge via the Internet at http://pubs.acs.org.…”

A Community Contribution Framework for Sharing Materials Data with Materials Project

“…More recent efforts, such as Materials Project [2], AFLOWlib [6], and others [7]- [11], typically include additional property data (generally computed) but do not currently have a contribution framework. Some repositories, such as NoMaD [12], iochem-bd [13], and the Materials Data Facility (MDF) [14], provide a shared repository of data, with potentially large experimental and structural data items, but many of these are in the early stages of development and without integrated data analysis capabilities over a core dataset. Our approach, by contrast, focuses on relatively small data contributions that can be joined with the carefully curated core dataset and extended with an integrated set of data analysis tools to provide a materials design environment.…”

“…The optional plots section can be used to request additional graphs or overwrite properties of the default ones based on the sections containing CSV tables. The plot axes are selected or changed by referring to the header of the table indicated in the table sub-key (lines [13][14][15][16][17]. The keys chosen for this section (x, y, kind, etc.)…”

Anions coordinating anions: analysis of the interaction between anionic Keplerate nanocapsules and their anionic ligands

“…76 A data set collection of input and output files is available online 77 in the ioChem-BD repository. 78 The energy decomposition analysis (EDA) as implemented in ADF was applied to divide the bonding energy between the capsule and its ligands into four parts: the Pauli repulsion, the electrostatic energy, the orbital interaction energy and finally the solvation energy contribution. Given the anionic nature of both the capsule and the ligands, the latter plays a key factor in balancing out excessive electrostatic and bonding repulsions.…”