W. D. S. Motherwell

Three dimensional structure of adenosine triphosphate.

The three dimensional structure of adenosine triphosphate in the hydrated disodium salt is reported to a resolution of 0.9 Å.

A database survey of molecular and crystallographic symmetry.

The point of contact between molecular and crystallographic symmetries is that of the Wyckoff position, the position at which a molecule resides in a crystal structure. These Wyckoff positions may have the same symmetry as the molecules, some symmetry in common with the molecules or no symmetry at all. Using CSDSymmetry [Yao et al. (2002). Acta Cryst. B58, 640-646], a relational database containing information pertaining to the symmetry of molecules and the crystal structures that play host to them, the distribution of molecules over Wyckoff positions and the occupancy of Wyckoff positions in crystal structures is presented. Analysis of these data has led to the characterization of some relationships between molecular and crystallographic symmetry.

Dipolar C[triple-bond]N...C[triple-bond]N interactions in organic crystal structures: database analysis and calculation of interaction energies.

The Cambridge Structural Database (CSD) has been used to study nonbonded interactions between dipolar cyano groups. The analysis shows that C[triple-bond]N...C[triple-bond]N interactions form in an analogous manner to those involving carbonyl groups, and with the same interaction motifs: a dominant antiparallel dimer (57.5%) together with smaller populations of perpendicular (19.4%) and sheared parallel (23.0%) motifs. Ab initio calculations using intermolecular perturbation theory (IMPT) show an attractive C[triple-bond]N...C[triple-bond]N interaction in the dominant antiparallel dimer, with E(t) = -20.0 kJ mol(-1) at d(C...N) = 3.30 A and with the motif having a shear angle close to 102 degrees . The antiparallel C[triple-bond]N...C[triple-bond]N interaction is therefore slightly weaker than the analogous C=O...C=O dimer (-23.5 kJ mol(-1)), but both interactions have attractive energies similar to that of a medium-strength hydrogen bond and, where sterically favoured, they are important in the stabilization of extended crystal structures.

Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge structural database

The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of -psi approximately varphi approximately 105 degrees allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH(2) spacers, this conformation leads to a parallel ladder with rings of equal size. If varphi approaches -60 degrees and psi 180 degrees, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH(2) spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks.

General method for the description, visualization and comparison of metal coordination spheres: geometrical preferences, deformations and interconversion pathways

The coordination sphere geometry of metal atoms (M) in their complexes with organic and inorganic ligands (L) is often compared with the geometry of archetypal forms for the appropriate coordination number, n in ML(n) species, by use of the k = n( n- 1)/2 L-M-L valence angles subtended at the metal centre. Here, a Euclidean dissimilarity metric, R(c)(x), is introduced as a one-dimensional comparator of these k-dimensional valence-angle spaces. The computational procedure for R(c)(x), where x is an appropriate archetypal form (e.g. an octahedron in ML(6) species), takes account of the atomic permutational symmetry inherent in ML(n) systems when no distinction is made between the individual ligand atoms. It is this permutational symmetry, of order n!, that precludes the routine application of multivariate analytical techniques, such as principal component analysis (PCA), to valence angle data for all but the lowest metal coordination numbers. It is shown that histograms of R(c)(x) values and, particularly, scatterplots of R(c)(x) values computed with respect to two or more different appropriate archetypal forms (e.g. tetrahedral and square-planar four-coordinations), provide information-rich visualizations of the observed geometrical preferences of metal coordination spheres retrieved from, e.g. the Cambridge Structural Database. These mappings reveal the highly populated clusters of similar geometries, together with the pathways that map their geometrical interconversions. Application of R(c)(x) analysis to the geometry of four- and seven-coordination spheres provides information that is at least comparable to, and in some cases is more complete than, that obtained by PCA.

Crystal and molecular structure of 17α-hydroxyandrost-4-en-3-one (epitestosterone)

Crystals of the title steroid are orthorhombic, a= 11·423(1), b= 20·151(1), c= 7·003(1)A, Z= 4, space group P212121. The structure has been determined by direct methods from diffractometer data and refined by full-matrix least-squares to a final R of 0·058 for 1646 reflections. All the ring junctions are trans/trans. The conformation of ring A is half-chair while that of rings B and C is chair. The cyclopentane ring D is a slightly distorted half-chair. The molecules are linked in the crystal structure ‘head-to-tail’ by a hydrogen bond between the C(17) hydroxy-group and the C(3) keto-group.

Parameterization of the close packing of molecules in the unit cell.

The box model of crystal packing describes unit cells in terms of a limited number of arrangements, or packing patterns, of molecular building blocks. Cell dimensions have been shown to relate to molecular dimensions in a systematic way. The distributions of pattern coefficients (cell length/molecular dimension) for thousands of structures belonging to P21/c, P1 , P212121, P21 and C2/c are presented and are shown to be entirely consistent with the box model of crystal packing. Contributions to the form of the histograms from molecular orientation and molecular overlap are discussed. Gaussian fitting of the histograms has led to the parameterization of close packing within the unit cell and it is shown that molecular crystal structures are very similar to one another at a fundamental level.

Automatic detection of molecular symmetry in the Cambridge Structural Database

A method for the detection of approximate molecular symmetry in crystal structures has been developed. The point-group symmetry is assigned to each molecule and the relevant symmetry elements can be visualized, superimposed on the molecule. The method has been validated against reference structures with exact symmetry subjected to small random perturbation.

X-ray crystal structure determination of the more laevorotatory diastereoisomer of 2′-O-tetrahydropyranyladenosine. Correlation of physical properties of tetrahydropyranyl ethers with absolute configuration

The structure of the more laevorotatory diastereoisomer of 2′-O-tetrahydropyranyladenosine has been determined by X-ray diffraction using direct methods. The final R factor is 3·9% for 1810 observed reflexions. Estimated standard deviations were 0·003–0·006 A in bond-lengths not involving hydrogen atoms. The adenosine dimensions and conformation are compared with other X-ray structure determinations. The absolute configuration of the acetal carbon centre [C(2″)] is deduced to be S, which agrees with indications from optical rotation measurements. The compound crystallises in space group P212121 with Z= 4 in a unit cell of dimensions: a= 10·942 ± 0·003, b= 28·235 ± 0·005, 5·292 ± 0·001 A.

Distribution of molecular centres in unit cells with respect to packing patterns.

Packing patterns, a new description of the limited number of possible arrangements of molecular building blocks in a unit cell, were assigned to many thousands of structures belonging to the space groups P2(1)/c, P1(-), P2(1)2(1)2(1), P2(1) and C2/c. The position of the molecular centre (in fractional coordinates) in the unit cell for these structures has been surveyed, with respect to the space group and the packing pattern. The results clearly show that the position at which the molecular centre is found in the unit cell is correlated with the packing pattern. The relationships between the orientation of the packing pattern in the unit cell and the symmetry operators of the space group are explored. Popular orientations of packing patterns within the unit cell are given.