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Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots—the formalization of cclib's intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects. [ABSTRACT FROM AUTHOR]

The interaction energy between intercalator and intercalant was analyzed based on crystallographic structure fragments of complexes involving cationic ethidium and proflavine. The electrostatic component constitutes the same fraction of the total energy for all three studied structures and cumulative atomic multipole moments interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures.

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. [ABSTRACT FROM AUTHOR]

Tailoring the size and surface chemistry of nanoparticles allows one to control their position in a block copolymer, but this is usually limited to one-dimensional distribution across domains. Here, the hierarchical assembly of poly(ethylene oxide)-stabilized gold nanoparticles (Au-PEO) into hexagonally packed clusters inside mesostructured ultrathin films of polystyrene- block-poly(methyl methacrylate) (PS- b-PMMA) is described. A close examination of the structural evolution at different nanoparticle filling 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 influence 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. [ABSTRACT FROM AUTHOR]

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. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]