Gregory P. Shields

CIF applications. XV. enCIFer: a program for viewing, editing and visualizing CIFs

The enCIFer program permits the location, reporting and correction of syntax and format violations in single- or multi-block crystallographic information files (CIFs). The program also permits the editing of existing individual or looped data items and the addition of new data in these categories, and provides data-entry wizards for the addition of two types of standard information for small-molecule structural studies, namely publication data and chemical and physical property information. Facilities for the graphical visualization and manipulation of structure(s) in a CIF are also provided.

Systematic analysis of the probabilities of formation of bimolecular hydrogen-bonded ring motifs in organic crystal structures

A methodology has been developed for characterising hydrogen-bonded ring motifs formed between two organic molecules without any prior knowledge of the topology or chemical constitution of the motifs. The method has been implemented by modifying the current Cambridge Structural Database (CSD) System programs. All intermolecular ring motifs comprising ⩽20 atoms formed with N—H···N, N—H···O, O—H···N and O—H···O hydrogen bonds in organic structures in the CSD have been classified. The 75 bimolecular motifs occurring in >12 structures in the CSD are described in terms of their graph sets and chemical functionalities. Motifs are ranked according to their frequency of occurrence and according to their probabilities of formation, i.e. their frequency relative to the number of possible motifs which could have formed. These probabilities provide insights into the relative robustness of known and potential supramolecular synthons.

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Visualization and characterization of non-covalent networks in molecular crystals: automated assignment of graph-set descriptors for asymmetric molecules

A method of visualizing intermolecular networks (for example, hydrogen-bonded networks) in the crystalline state has been developed, based on the concept of link atoms, i.e. those atoms deemed to be in contact with each unique molecule or ion in the crystal chemical unit (CCU). Extension of a structure using each of these primary links can be achieved, enabling the generation and investigation of extended networks. Algorithms have been developed for the automatic assignment of graph-set notation for patterns up to second level, i.e. those involving one or two crystallographically independent non-covalent bonds, in the absence of internal crystallographic symmetry in the unique molecules of the CCU. The self, ring, chain and discrete motifs may be displayed by highlighting the atoms and bonds comprising the pattern. These methodologies have been implemented in the Cambridge Structural Database program PLUTO.

The assignment and validation of metal oxidation states in the Cambridge Structural Database

A methodology has been developed for the semi-automatic assignment and checking of formal oxidation states for metal atoms in the majority of metallo-organic complexes stored in the Cambridge Structural Database (CSD). The method uses both chemical connectivity and bond-length data, via ligand donor group templates and bond-valence sums, respectively. In order to use bond-length data, the CSD program QUEST has been modified to allow the coordination sphere of metal atoms to be recalculated using user-defined criteria at search time. The new methodology has been used successfully to validate the +1, +2 and +3 oxidation states in 743 four-coordinate copper complexes in the CSD for which atomic coordinates are available in ca 99% of structures using one or other method, and both succeed for >86% of structures.

Intramolecular hydrogen bonds: common motifs, probabilities of formation and implications for supramolecular organization

A systematic survey of the Cambridge Structural Database (CSD) has identified all intramolecular hydrogen-bonded ring motifs comprising less than 20 atoms with N and O donors and acceptors. The probabilities of formation P(m) of the 50 most common motifs, which chiefly comprise five- and six-membered rings, have been derived by considering the number of intramolecular motifs which could possibly form. The most probable motifs (P(m) > 85%) are planar conjugated six-membered rings with a propensity for resonance-assisted hydrogen bonding and these form the shortest contacts, whilst saturated six-membered rings typically have P(m) < 10%. The influence of intramolecular-motif formation on intermolecular hydrogen-bond formation has been assessed for a planar conjugated model substructure, showing that a donor-H is considerably less likely to form an intermolecular bond if it forms an intramolecular one. On the other hand, the involvement of a carbonyl acceptor in an intramolecular bond does not significantly affect its ability to act as an intermolecular acceptor and thus carbonyl acceptors display a substantially higher inclination for bifurcation if one hydrogen bond is intramolecular.

Implications of molecular and materials structure for new technologies

Preface. List of Contributors. Into the New Millennium: the Present and Future of Crystal Structure Analysis J.D. Dunitz. Modern Neutron Diffraction Methods C.C. Wilson. Electron Densities and Electrostatic Properties of Materials from High Resolution X Ray Diffraction C. Lecomte. Dynamic Processes and Disorder in Materials as seen by Temperature-Dependent Diffraction Experiments H.-B. Buergi, S.C. Capelli. Atomic Displacement Parameters, Vibrational Spectra and Thermodynamic Functions for Crystals: a Strong Connection C.M. Gramaccioli. Molecular Mechanics Modeling of Transition Metal Compounds P. Comba. Modeling Structural, Spectroscopic and Redox Properties of Transition Metal Compounds P. Comba. Molecules in Crystals - What Makes them Different? K. Hermansson. A New ab initio Powder Method and Profile Refinement in Materials Design: Application to Polymer Electrolytes P. Bruce, et al. Quantum Mechanical Modeling of Structure Evolution of Transition Metal Clusters and Metallocarbohedrenes Hansong Cheng, Lai-Sheng Wang. Solid-State Reactivity and Implications for Catalytic Processes E.V. Boldyreva. Weak Interactions in Molecular Crystals J.D. Dunitz. Weak Hydrogen Bonds T. Steiner. Direct and Indirect Roles of Metal Centres in Hydrogen Bonding L. Brammer. Supramolecular Organization in Organometallic Crystals F. Grepioni, D. Braga. Theoretical Approaches to the Study of Non-Bonded Interactions S.L. Price. Intermolecular Interactions in Molecular Crystals Studied by ab initio Methods from Isolated Interactions to Patterns and Crystals J.J. Novoa. Systematic Study of Crystal Packing C.P. Brock. Molecular Shape as a Design Criterion R.E. Davis, et al. Graph Set Analysis of Hydrogen Bond Motifs J. Bernstein, R.E. Davis. Crystallographic Databases and Knowledge Bases in Materials Design F.H. Allen, G.P. Shields. Computational Approaches to Crystal Structure and Polymorph Prediction F.J.J. Leusen, et al. Developing Methods of Crystal Structure and Polymorph Prediction S.L. Price. Current Challenges in Crystal Engineering G.R. Desiraju. Index.

Crystal Engineering and Chloro-Methyl Interchange—a CSD Analysis

Abstract A search method for investigating the extent to which chloro-methyl interchange is exhibited by crystal structures deposited with the Cambridge Crystallographic Database is presented. Using the October 1998 release with 190,307 data entries, 105 pairs were identified for which there was a common molecular framework, differing only in the presence of a chloro or methyl group. Approximately 30% appear to demonstrate isotructural packing arrangements. Two examples within the database that were found not to show Cl-Me interchange were subsequently examined from the viewpoint of structural mimicry and the formation of mixed crystals.

Automated assignment of graph-set descriptors for crystallographically symmetric molecules

Algorithms for the automatic assignment of graph-set notation for intermolecular networks have been extended to molecules having internal crystallographic symmetry, for patterns up to the second level. This provides a means of achieving systematic and consistent assignments for networks containing symmetric molecules. These methodologies have been implemented in the program RPLUTO. Examples are given of the application of the method to a number of molecules with hydrogen-bonded and other intermolecular networks, illustrating the diversity of the patterns that occur.

Structure correlation study of four-coordinate copper(I) and (II) complexes

The geometries of four-coordinate CuI and CuII complexes in the Cambridge Structural Database (CSD) have been analysed systematically and compared using symmetry-deformation coordinates and principal component analysis. The observed stereochemistries have been rationalized in terms of the d-electron configurations, interligand repulsion and pi-bonding effects. The results confirm that the majority of four-coordinate copper(I) complexes in the CSD adopt tetrahedral geometries and deviations from tetrahedral symmetry are caused by the presence of chelating ligands or by the incorporation of copper centres into dimeric or polymeric structures. Four-coordinate copper(II) complexes generally adopt geometries close to square planar; this is particularly evident for bis(chelate) complexes where pi-bonding is important. Distortions towards tetrahedral geometries are attributable to steric interactions of bulky substituents in the bidentate ligands.