Karol M. Langner

cclib: a library for package-independent computational chemistry algorithms.

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.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

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.

Intriguing relations of interaction energy components in stacked nucleic acids

Major components of the interaction energy that define several approximate levels starting from second order Möller-Plesset theory were studied for 58 stacked nucleic acid dimers. They included typical B-DNA and A-DNA structures, and selected published geometries. A survey of the various terms yields an unexpected correlation between the Pauli exchange and dispersion or correlation terms, which holds for each class of similar planar geometries and for various basis sets. The geometries that exhibit these correlations span a specific range of molecular overlaps when compared to a model benzene-pyridine stacked dimer. Also, the relationship between electrostatic interactions and MP2 stabilization energies reported earlier is confirmed and a prediction interval of practical relevance is estimated.

Mesoscale modeling of block copolymer nanocomposites

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.

Electric Field Induced Selective Disordering in Lamellar Block Copolymers

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.

Selective disordering of lamella-forming diblock copolymers under an electric field

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.

Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances

The relative stability of biologically relevant, hydrogen bonded complexes with shortened distances can be assessed at low cost by the electrostatic multipole term alone more successfully than by ab initio methods. These results imply that atomic multipole moments may help improve ligand–receptor ranking predictions, particularly in cases where accurate structural data are not available.

The Ethidium–UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State

We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, and correlation components. Various pairwise interaction models built from chemically intuitive fragments reproduce within a few percent values obtained when treating the intercalation site as a whole. Gas phase results are very sensitive to the charge state of the two phosphate groups, with the electrostatic term nearly tripling when the counterions are removed. But this is largely compensated by solvation, an effect represented here within the polarizable continuum model. In a few cases, more diffuse and larger basis sets as well as QCISD(T) corrections were applied in an effort to estimate plausible ethidium-nucleobase electron correlation effects.

Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography

Using all available metal-containing organic compound structures in the Cambridge Structural Database, a novel data-driven method to derive bond-valence R 0 parameters was developed. While confirming almost all reference literature values, two distinct populations of FeII—N and FeIII—N bonds are observed, which are interpreted as low-spin and high-spin states of the coordinating iron. Based on the R 0 parameters derived here, guidelines for the modeling of iron–ligand distances in macromolecular structures are suggested.

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

Bacteria are increasingly resistant to existing antibiotics, which target a narrow range of pathways. New methods are needed to identify targets, including repositioning targets among distantly related species. We developed a novel combination of systems and structural modeling and bioinformatics to reposition known antibiotics and targets to new species. We applied this approach to Mycoplasma genitalium, a common cause of urethritis. First, we used quantitative metabolic modeling to identify enzymes whose expression affects the cellular growth rate. Second, we searched the literature for inhibitors of homologs of the most fragile enzymes. Next, we used sequence alignment to assess that the binding site is shared by M. genitalium, but not by humans. Lastly, we used molecular docking to verify that the reported inhibitors preferentially interact with M. genitalium proteins over their human homologs. Thymidylate kinase was the top predicted target and piperidinylthymines were the top compounds. Further work is needed to experimentally validate piperidinylthymines. In summary, combined systems and structural modeling is a powerful tool for drug repositioning.