The program Mercury, developed by the Cambridge Crystallographic Data Centre, is designed primarily as a crystal structure visualization tool. A new module of functionality has been produced, called the Materials Module, which allows highly customizable searching of structural databases for intermolecular interaction motifs and packing patterns. This new module also includes the ability to perform packing similarity calculations between structures containing the same compound. In addition to the Materials Module, a range of further enhancements to Mercury has been added in this latest release, including void visualization and links to ConQuest, Mogul and IsoStar.

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

https://journals.iucr.org/b/issues/2016/02/00/bm5086/bm5086.pdf

The Cambridge Structural Database

In the last few years the analysis of molecular crystal structures using tools based on Hirshfeld surfaces has rapidly gained in popularity. This approach represents an attempt to venture beyond the current paradigm—internuclear distances and angles, crystal packing diagrams with molecules represented via various models, and the identification of close contacts deemed to be important—and to view molecules as “organic wholes”, thereby fundamentally altering the discussion of intermolecular interactions through an unbiased identification of all close contacts.

Hirshfeld surface analysis

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

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Mercury 4.0: from visualization to analysis, design and prediction

Cellulose samples are routinely analyzed by X-ray diffraction to determine their crystal type (polymorph) and crystallinity. However, the connection is seldom made between those efforts and the crystal structures of cellulose that have been proposed with synchrotron X-radiation and neutron diffraction over the past decade or so. In part, this desirable connection is thwarted by the use of different conventions for description of the unit cells of the crystal structures. In the present work, powder diffraction patterns from cellulose Iα, Iβ, II, IIII, and IIIII were calculated based on the published atomic coordinates and unit cell dimensions contained in modified “crystal information files” (.cif) that are supplied in the Supplementary Information. The calculations used peak widths at half maximum height of both 0.1 and 1.5° 2θ, providing both highly resolved indications of the contributions of each contributing reflection to the observable diffraction peaks as well as intensity profiles that more closely resemble those from practical cellulose samples. Miller indices are shown for each contributing peak that conform to the convention with c as the fiber axis, a right-handed relationship among the axes and the length of a < b. Adoption of this convention, already used for crystal structure determinations, is also urged for routine studies of polymorph and crystallinity. The calculated patterns are shown with and without preferred orientation along the fiber axis. Diffraction intensities, output by the Mercury program from the Cambridge Crystallographic Data Centre, have several uses including comparisons with experimental data. Calculated intensities from different polymorphs can be added in varying proportions using a spreadsheet program to simulate patterns such as those from partially mercerized cellulose or various composites.

Idealized powder diffraction patterns for cellulose polymorphs

The probability of organic compounds crystallising as hydrates increases with increasing number of polar chemical groups in the molecule. The extended patterns of H-bonding involving chemical groups and water molecules have been studied and classified. The most frequent ring, chain, tape and layer patterns displayed between the water molecules alone in organic molecular crystals are also predominant patterns in the larger H-bond network when other donor/acceptors are included.

Extended motifs from water and chemical functional groups in organic molecular crystals

A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

COMPACK: a program for identifying crystal structure similarity using distances

Water oligomers in crystal hydrates--what's news and what isn't?

Lattice energy searches for theoretical low-energy crystal forms are presented for 50 small organic molecules, and we compare the experimentally observed crystal forms to these lists of hypothetical polymorphs. For each known crystal, the relative stability is calculated with respect to the global minimum energy structure, and we determine the number of unobserved structures lower in energy than the experimental form. The distributions of these relative energies and their rankings in the predicted lists are used to determine the efficacy of lattice energy minimization in crystal structure prediction. Although a simple form for the interaction energies has been used, the calculations produce almost a third of the known crystals as the global minimum in energy, and approximately a half of the known structures are within 1 kJ/mol of the global minimum. Molecules with no hydrogen-bonding capacity are most likely to be found close to the global minimum in lattice energy, while increasing the number of possible...

James A. Chisholm

Papers

Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures

Extended motifs from water and chemical functional groups in organic molecular crystals

COMPACK: a program for identifying crystal structure similarity using distances

Water oligomers in crystal hydrates--what's news and what isn't?

An Assessment of Lattice Energy Minimization for the Prediction of Molecular Organic Crystal Structures