Free volume in ionic liquids: a connection of experimentally accessible observables from PALS and PVT experiments with the molecular structure from XRD data

In the current work, free volume concepts, primarily applied to glass formers in the literature, were transferred to ionic liquids (ILs). A series of 1-butyl-3-methylimidazolium ([C4MIM](+)) based ILs was investigated by Positron Annihilation Lifetime Spectroscopy (PALS). The phase transition and dynamic properties of the ILs [C4MIM][X] with [X](-) = [Cl](-), [BF4](-), [PF6](-), [OTf](-), [NTf2](-) and [B(hfip)(4)](-) were reported recently (Yu et al., Phys. Chem. Chem. Phys., 2012, 14, 6856-6868). In this subsequent work, attention was paid to the connection of the free volume from PALS (here the mean hole volume, ) with the molecular structure, represented by volumes derived from X-ray diffraction (XRD) data. These were the scaled molecular volume V-m,V-scaled and the van der Waals volume V-vdw. Linear correlations of at the "knee'' temperature ((T-k)) with V-m,V-scaled and V-vdw gave good results for the [C4MIM](+) series. Further relationships between volumes from XRD data with the occupied volume V-occ determined from PALS/PVT (Pressure Volume Temperature) measurements and from Sanchez-Lacombe Equation of State (SL-EOS) fits were elaborated (V-occ(SL-EOS) approximate to 1.63 V-vdw, R-2 = 0.981 and V-occ(SL-EOS) approximate to 1.12 V-m,V-scaled, R-2 = 0.980). Finally, the usability of V-m,V-scaled was justified in terms of the Cohen-Turnbull (CT) free volume theory. Empirical CT type plots of viscosity and electrical conductivity showed a systematic increase in the critical free volume with molecular size. Such correlations allow descriptions of IL properties with the easily accessible quantity V-m,V-scaled within the context of the free volume

Standards-based metadata management for molecular simulations

State-of-the-art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high-performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics