J. Appl. Cryst.の発刊に際して

A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org
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Open Babel: An open chemical toolbox

Synthesis of metal-organic frameworks (MOFs): routes to various MOF topologies, morphologies, and composites.

We have recently described a remarkable new way of exploring packing modes and intermolecular interactions in molecular crystals using a novel partitioning of crystal space. These molecular Hirshfeld surfaces reflect intermolecular interactions in a novel visual manner, offering a hitherto unseen picture of molecular shape in a crystalline environment. The surfaces encode information about all intermolecular interactions simultaneously, but sophisticated interactive graphics are required in order to extract the information most efficiently. To overcome this we have devised a two-dimensional mapping which summarizes quantitatively the nature and type of intermolecular interaction experienced by a molecule in the bulk, and presents it in a convenient graphical format. The mapping takes advantage of the triangulation of the Hirshfeld surfaces, and plots the fraction of points on the surface as a function of the closest distances from the point to nuclei inside and outside the surface.
In this manner all interaction types (for example, hydrogen bonding, close and distant van der Waals contacts, C–H⋯π interactions, π–π stacking) are readily identifiable, and it becomes a straightforward matter to classify molecular crystals by the nature of interactions, and to rapidly identify similarities and differences which can become obscured when examining crystal packing diagrams. These plots are a novel visual representation of all the intermolecular interactions simultaneously, and are unique for a given crystal structure and polymorph. Applications to a wide variety of molecular crystals and intermolecular interactions are presented, including polymorphic systems, as well as crystals where Z′ > 1.

Fingerprinting intermolecular interactions in molecular crystals

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

The Halogen Bond

Poor mechanical properties of paracetamol are improved through the strategy of cocrystal formation. Mechanochemical screening by liquid-assisted grinding generated four cocrystals of paracetamol that readily form tablets by direct compression. Computational studies reveal the mechanical properties can be related to structural features, before all the formation of hydrogen-bonded layers.

Improving Mechanical Properties of Crystalline Solids by Cocrystal Formation: New Compressible Forms of Paracetamol

Freshly ground: Improved mechanochemical methodologies, such as liquid-assisted grinding and ion- and liquid-assisted grinding enable the rapid and topologically selective synthesis of porous and nonporous zeolitic imidazolate frameworks with diverse topologies, at room temperature and directly from zinc oxide.

Rapid Room‐Temperature Synthesis of Zeolitic Imidazolate Frameworks by Using Mechanochemistry

A set of complete, reliable cocrystal structures was extracted from the Cambridge Structural Database, and molecular descriptors, usually used in quantitative structure-activity relationship studies, were calculated for each molecule. The resulting database describes pairs of molecules that form cocrystals with each other in terms of their calculated molecular properties. Statistical analysis of the data was performed to identify properties that tend to be similar or complementary for such pairs of molecules. The strongest descriptor correlations found relate to the shape and polarity of cocrystal formers. Hydrogen bond donor and acceptor counts of cocrystal formers, on the other hand, show no obvious statistical relationship.

Cambridge Structural Database Analysis of Molecular Complementarity in Cocrystals

Liquid-assisted grinding enabled the rapid and environmentally-friendly conversion of a simple and inexpensive metal oxide precursor into a variety of metal–organic materials, demonstrated by the quantitative construction of six coordination polymers and porous frameworks from a mixture of ZnO and fumaric acid.

Mechanochemical conversion of a metal oxide into coordination polymers and porous frameworks using liquid-assisted grinding (LAG)

A database study of 34 770 accurate organic crystal structures reveals that the most important factor determining a higher frequency of hydrates is the sum of the average donor and acceptor counts for the functional groups. Different parameter forms for donor/acceptor properties were investigated for correlation with formation of hydrates, and are discussed. We did not find that the donor/acceptor ratio or the molecular weight significantly affects the hydrate formation. We also examined a wide range of calculated molecular properties and found that increasing polar surface is correlated with increasing hydrate formation. The water environment pattern of donor and acceptor hydrogen bonds in the crystal is influenced by the donor/acceptor ratio of the molecule.

László Fábián

Papers

Improving Mechanical Properties of Crystalline Solids by Cocrystal Formation: New Compressible Forms of Paracetamol

Rapid Room‐Temperature Synthesis of Zeolitic Imidazolate Frameworks by Using Mechanochemistry

Cambridge Structural Database Analysis of Molecular Complementarity in Cocrystals

Mechanochemical conversion of a metal oxide into coordination polymers and porous frameworks using liquid-assisted grinding (LAG)

Organic crystal hydrates : what are the important factors for formation