There are now a wide variety of packages for electronic structure calculations, each of which differs in the algorithms implemented and the output format. Many computational chemistry algorithms are only available to users of a particular package despite being generally applicable to the results of calculations by any package. Here we present cclib, a platform for the development of package-independent computational chemistry algorithms. Files from several versions of multiple electronic structure packages are automatically detected, parsed, and the extracted information converted to a standard internal representation. A number of population analysis algorithms have been implemented as a proof of principle. In addition, cclib is currently used as an input filter for two GUI applications that analyze output files: PyMOlyze and GaussSum.

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessibleviathe web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics projects.

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

BackgroundThe Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards.ResultsThis contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry.ConclusionsWe show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

Tailoring the size and surface chemistry of nanoparticles allows one to control their position in a block copolymer, but this is usually limited to onedimensional distribution across domains. Here, the hierarchical assembly of poly(ethylene oxide)-stabilized gold nanoparticles (Au-PEO) into hexagonally packed clusters inside mesostructured ultrathin fi lms of polystyrene-blockpoly(methyl methacrylate) (PS-b -PMMA) is described. A close examination of the structural evolution at different nanoparticle fi lling fractions and PEO ligand molecular weights suggests that the mechanism leading to this structure-within-structure is the existence of two phase separation processes operating on different time scales. The length of the PEO ligand is shown to infl uence not only the interparticle distances but also the phase separation processes. These conclusions are supported by novel mesoscopic simulations, which provide additional insight into the kinetic and thermodynamic factors that are responsible for this behavior. Figure 1 . HR-SEM images, at two magnifi cations, of ultrathin PSb -PMMA/Au-PEO fi lms after 14 h of annealing in chloroform vapor, with different lengths of the PEO ligands: a,b) 5 kDa ( σ = 460 ± 40 NP μ m − 2 ) and c,d) 20 kDa ( σ = 320 ± 10 NP μ m − 2 ). Black and gray domains correspond to the PMMA and PS domains, respectively.

External electric fields align nanostructured block copolymers by either rotation of grains or nucleation and growth depending on how strongly the chemically distinct block copolymer components are segregated. In close vicinity to the order-disorder transition, theory and simulations suggest a third mechanism: selective disordering. We present a time-resolved small-angle X-ray scattering study that demonstrates how an electric field can indeed selectively disintegrate ill-aligned lamellae in a lyotropic block copolymer solution, while lamellae with interfaces oriented parallel to the applied field prevail. The present study adds an additional mechanism to the experimentally corroborated suite of mechanistic pathways, by which nanostructured block copolymers can align with an electric field. Our results further unveil the benefit of electric field assisted annealing for mitigating orientational disorder and topological defects in block copolymer mesophases, both in close vicinity to the order-disorder transition and well below it.

Nanoadditives alter the properties of pure block copolymers, through an interplay of entropic, enthalpic and kinetic factors at competing length and time scales. A fundamental understanding of these factors is considered decisive for taming block copolymer nanocomposites, since even modest changes in design parameters can impact the final material. At the same time, analytical and computational approaches have not yet reached the maturity required for an integrated study of all relevant aspects. Heterogeneity, local irregularities and dynamic behavior-these are the most challenging issues facing theory and simulations in the quest for rational design. In this review, we discuss the state of mesoscopic modeling for block copolymer nanocomposites, and cover relevant literature from at least the last five years, during which developments have taken off.

Self-assembled block polymers show great potential to serve as templates for the fabrication of nanoscale structures for devices, provided that structural features such as defects and global orientation can be fully and efficiently controlled. The most efficient way to control these features is by application of an electric field, to orient features parallel to the electric field. Several aspects of the thermodynamic and kinetic factors that determine the reorientation dynamics have been studied in recent years and are increasingly understood. Current experiments focus on reorientation close to the order-disorder transition (ODT) temperature, where an efficient mechanism involving selective disordering is long anticipated but subject to lively debate. Here, we complement the increasing experimental understanding by a detailed and unifying computational analysis of all distinct microscopic stages in this new reorientation mechanism. The unification step originates from the comparison of two different models, one based on a molecular description and the other phenomenological. The results have a general character and may also serve as a stepping stone for understanding microscopic response pathways due to other kinds of deformation, such as mechanical stress or shear. We find that reorientation is most effective for temperatures that are slightly below ODT, at which the system is slightly demixed and the balance between surface tension and the ponderomotive force is optimal. © 2011 The Royal Society of Chemistry