The Continuum Between Hexagonal Planar and Trigonal Planar Geometries.

New heterometallic hydride complexes that involve the addition of {Mg-H} and {Zn-H} bonds to group 10 transition metals (Pd, Pt) are reported. The side-on coordination of a single {Mg-H} to Pd forms a well-defined σ-complex. In contrast, addition of three {Mg-H} or {Zn-H} bonds to Pd or Pt results in the formation of planar complexes with subtly different geometries. We compare their structures through experiment (X-ray diffraction, neutron diffraction, multinuclear NMR), computational methods (DFT, QTAIM, NCIPlot), and theoretical analysis (MO diagram, Walsh diagram). These species can be described as snapshots along a continuum of bonding between ideal trigonal planar and hexagonal planar geometries.

Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain.

CREBBP (CBP/KAT3A) and its paralogue EP300 (KAT3B) are lysine acetyltransferases (KATs) that are essential for human development. They each comprise 10 domains through which they interact with >400 proteins, making them important transcriptional co-activators and key nodes in the human protein-protein interactome. The bromodomains of CREBBP and EP300 enable the binding of acetylated lysine residues from histones and a number of other important proteins, including p53, p73, E2F, and GATA1. Here, we report a work to develop a high-affinity, small-molecule ligand for the CREBBP and EP300 bromodomains [(-)-OXFBD05] that shows >100-fold selectivity over a representative member of the BET bromodomains, BRD4(1). Cellular studies using this ligand demonstrate that the inhibition of the CREBBP/EP300 bromodomain in HCT116 colon cancer cells results in lowered levels of c-Myc and a reduction in H3K18 and H3K27 acetylation. In hypoxia (<0.1% O2), the inhibition of the CREBBP/EP300 bromodomain results in the enhanced stabilization of HIF-1α.

The partial dehydrogenation of aluminium dihydrides.

The reactions of a series of ß-diketiminate stabilised aluminium dihydrides with ruthenium bis(phosphine), palladium bis(phosphine) and palladium cyclopentadienyl complexes is reported. In the case of ruthenium, alane coordination occurs with no evidence for hydrogen loss resulting in the formation of ruthenium complexes with a pseudo-octahedral geometry and cis-relation of phosphine ligands. These new ruthenium complexes have been characterised by multinuclear and variable temperature NMR spectroscopy, IR spectroscopy and single crystal X-ray diffraction. In the case of palladium, a series of structural snapshots of alane dehydrogenation have been isolated and crystallographically characterised. Variation of the palladium precursor and ligand on aluminium allows kinetic control over reactivity and isolation of intermetallic complexes that contain new Pd-Al and Pd-Pd interactions. These complexes differ by the ratio of H : Al (2 : 1, 1.5 : 1 and 1 : 1) with lower hydride content species forming with dihydrogen loss. A combination of X-ray and neutron diffraction studies have been used to interrogate the structures and provide confidence in the assignment of the number and position of hydride ligands. 27Al MAS NMR spectroscopy and calculations (DFT, QTAIM) have been used to gain an understanding of the dehydrogenation processes. The latter provide evidence for dehydrogenation being accompanied by metal-metal bond formation and an increased negative charge on Al due to the covalency of the new metal-metal bonds. To the best of our knowledge, we present the first structural information for intermediate species in alane dehydrogenation including a rare neutron diffraction study of a palladium-aluminium hydride complex. Furthermore, as part of these studies we have obtained the first SS 27Al NMR data on an aluminium(i) complex. Our findings are relevant to hydrogen storage, materials chemistry and catalysis.

A hexagonal planar transition-metal complex.

Transition-metal complexes are widely used in the physical and biological sciences. They have essential roles in catalysis, synthesis, materials science, photophysics and bioinorganic chemistry. Our understanding of transition-metal complexes originates from Alfred Werner's realization that their three-dimensional shape influences their properties and reactivity1, and the intrinsic link between shape and electronic structure is now firmly underpinned by molecular-orbital theory2-5. Despite more than a century of advances in this field, the geometries of transition-metal complexes remain limited to a few well-understood examples. The archetypal geometries of six-coordinate transition metals are octahedral and trigonal prismatic, and although deviations from ideal bond angles and bond lengths are frequent6, alternative parent geometries are extremely rare7. The hexagonal planar coordination environment is known, but it is restricted to condensed metallic phases8, the hexagonal pores of coordination polymers9, or clusters that contain more than one transition metal in close proximity10,11. Such a geometry had been considered12,13 for [Ni(PtBu)6]; however, an analysis of the molecular orbitals suggested that this complex is best described as a 16-electron species with a trigonal planar geometry14. Here we report the isolation and structural characterization of a simple coordination complex in which six ligands form bonds with a central transition metal in a hexagonal planar arrangement. The structure contains a central palladium atom surrounded by three hydride and three magnesium-based ligands. This finding has the potential to introduce additional design principles for transition-metal complexes, with implications for several scientific fields.

Heteroatom substitution effects in spin crossover dinuclear complexes.

We probe the effect of heteroatom substitution on the spin crossover (SCO) properties of dinuclear materials of the type [Fe2(NCX)4(R-trz)5]·S (X = S, Se; S = solvent; R-trz = (E)-N-(furan-2-ylmethylene)-4H-1,2,4-triazol-4-amine (furtrz); (E)-N-(thiophen-2-ylmethylene)-4H-1,2,4-triazole-4-amine (thtrz)). For the furtrz family ([Fe2(NCX)4(furtrz)5]·furtrz·MeOH; X = S (furtrz-S) and X = Se (furtrz-Se)) gradual and incomplete one-step SCO transitions are observed (furtrz-S (T1/2 = 172 K) and furtrz-Se (T1/2 = 205 K)) and a structural evolution from [HS-HS] to [HS-LS] per dinuclear species. Contrasting this, within the thtrz family ([Fe2(NCX)4(thtrz)5]·4MeOH; X = S (thtrz-S) and X = Se (thtrz-Se)) more varied SCO transitions are observed, with thtrz-S being SCO-inactive (high spin) and thtrz-Se showing a rare complete two-step SCO transition (T1/2(1,2) = 170, 200 K) in which the FeII sites transition from [HS-HS] to [HS-LS] to [LS-LS] per dinuclear unit with no long range ordering of spin-states at the intermediate plateau. Detailed structure-function analyses have been conducted within this growing dinuclear family to rationalise these diverse spin-switching properties.

HUG and SQUEEZE: using CRYSTALS to incorporate resonant scattering in the SQUEEZE structure-factor contributions to determine absolute structure.

The resonant-scattering contributions to single-crystal X-ray diffraction data enable the absolute structure of crystalline materials to be determined. Crystal structures can be determined even if they contain considerably disordered regions because a correction is available via a discrete Fourier transform of the residual electron density to approximate the X-ray scattering from the disordered region. However, the corrected model cannot normally account for resonant scattering from atoms in the disordered region. Straightforward determination of absolute structure from crystals where the strongly resonantly scattering atoms are not resolved has therefore not been possible. Using an approximate resonant-scattering correction to the X-ray scattering from the disordered regions, we have developed and tested a procedure (HUG) to recover the absolute structure using conventional Flack x refinement or other post-refinement determination methods. Results show that in favourable cases the HUG method works well and the absolute structure can be correctly determined. It offers no useful improvement in cases where the original correction for the disordered region scattering density is problematic, for example, when a large fraction of the scattering density in the crystal is disordered, or when voids are not occupied equally by the disordered species. Crucially, however, if the approach does not work for a given structure, the statistics for the absolute structure measures are not improved, meaning it is unlikely to lead to misassignment of absolute structure.

Beyond Rotatable Bond Counts: Capturing 3D Conformational Flexibility in a Single Descriptor.

A new molecular descriptor, nConf20, based on chemical connectivity, is presented which captures the accessible conformational space of a molecule. Currently the best available two-dimensional descriptors for quantifying the flexibility of a particular molecule are the rotatable bond count (RBC) and the Kier flexibility index. We present a descriptor which captures this information by sampling the conformational space of a molecule using the RDKit conformer generator. Flexibility has previously been identified as a key feature in determining whether a molecule is likely to crystallize or not. For this application, nConf20 significantly outperforms previously reported single-variable classifiers and also assists rule-based analysis of black-box machine learning classification algorithms.

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

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

The application of inelastic neutron scattering to investigate the interaction of methyl propanoate with silica.

A modern industrial route for the manufacture of methyl methacrylate involves the reaction of methyl propanoate and formaldehyde over a silica-supported Cs catalyst. Although the process has been successfully commercialised, little is known about the surface interactions responsible for the forward chemistry. This work concentrates upon the interaction of methyl propanoate over a representative silica. A combination of infrared spectroscopy, inelastic neutron scattering, DFT calculations, X-ray diffraction and temperature-programmed desorption is used to deduce how the ester interacts with the silica surface.

Compositional dependence of anomalous thermal expansion in perovskite-like ABX3 formates.

The compositional dependence of thermal expansion behaviour in 19 different perovskite-like metal-organic frameworks (MOFs) of composition [A(I)][M(II)(HCOO)3] (A = alkylammonium cation; M = octahedrally-coordinated divalent metal) is studied using variable-temperature X-ray powder diffraction measurements. While all systems show essentially the same type of thermomechanical response-irrespective of their particular structural details-the magnitude of this response is shown to be a function of A(I) and M(II) cation radii, as well as the molecular anisotropy of A(I). Flexibility is maximised for large M(II) and small A(I), while the shape of A(I) has implications for the direction of framework hingeing.

Crystal structures of increasingly large molecules: meeting the challenges with CRYSTALS software.

BACKGROUND: The size and complexity of molecules being studied by single crystal diffraction is growing year by year, resulting in an increase in the difficulties encountered during structure determination. From the crystallisation itself and sample handling, to structure solution and refinement, specific problems due to larger molecules are discussed. RESULTS: During refinement, several methods are available to deal with the problems encountered with large structures within the software Crystals. Hydrogens atoms can neither be found easily nor refined freely, but restraints can be applied automatically. Special scattering factors can be used to model complex disorder. Finally chemical information can be included in the form of restraints in order to help the determination of a good model. Multicollinearity problems are more likely in the refinement of large structures; to some extent more precise and accurate algorithms can help. Also, if the global minimum is less well defined, faster refinement enables more cycles to be carried out, a necessity for good convergence. The efficiency of the algorithms in Crystals have been increased to help address these issues. CONCLUSIONS: Thus, crystal structures are getting larger and their complexity is increasing. Recent developments in precision and speed during the least squares in Crystals is helping the structural scientist to deal with larger structures more efficiently.

DetOx: a program for determining anomalous scattering factors of mixed-oxidation-state species.

Overlapping absorption edges will occur when an element is present in multiple oxidation states within a material. DetOx is a program for partitioning overlapping X-ray absorption spectra into contributions from individual atomic species and computing the dependence of the anomalous scattering factors on X-ray energy. It is demonstrated how these results can be used in combination with X-ray diffraction data to determine the oxidation state of ions at specific sites in a mixed-valance material, GaCl(2).

ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics.

We present ElectroShape, a novel ligand-based virtual screening method, that combines shape and electrostatic information into a single, unified framework. Building on the ultra-fast shape recognition (USR) approach for fast non-superpositional shape-based virtual screening, it extends the method by representing partial charge information as a fourth dimension. It also incorporates the chiral shape recognition (CSR) method, which distinguishes enantiomers. It has been validated using release 2 of the Directory of useful decoys (DUD), and shows a near doubling in enrichment ratio at 1% over USR and CSR, and improvements as measured by Receiver Operating Characteristic curves. These improvements persisted even after taking into account the chemotype redundancy in the sets of active ligands in DUD. During the course of its development, ElectroShape revealed a difference in the charge allocation of the DUD ligand and decoy sets, leading to several new versions of DUD being generated as a result. ElectroShape provides a significant addition to the family of ultra-fast ligand-based virtual screening methods, and its higher-dimensional shape recognition approach has great potential for extension and generalisation.

Steviamine, a new class of indolizidine alkaloid [(1R,2S,3R,5R,8aR)-3-hydroxy-meth-yl-5-methyl-octa-hydro-indolizine-1,2-diol hydro-bromide].

X-ray crystallographic analysis of the title hydro-bromide salt, C(10)H(20)N(+)·Br(-), of (1R,2S,3R,5R,8aR)-3-hydroxy-meth-yl-5-methyl-octa-hydro-indolizine-1,2-diol defines the absolute and relative stereochemistry at the five chiral centres in steviamine, a new class of polyhydroxy-lated indolizidine alkaloid isolated from Stevia rebaudiana (Asteraceae) leaves. In the crystal structure, mol-ecules are linked by inter-molecular O-H⋯Br and N-H⋯Br hydrogen bonds, forming double chains around the twofold screw axes along the b-axis direction. Intra-molecular O-H⋯O inter-actions occur.

Structure and hydrogen bonding in 2,4-dihydroxybenzoic acid at 90, 100, 110 and 150 K; a theoretical and single-crystal X-ray diffraction study.

A new polymorph of 2,4-dihydroxybenzoic acid is reported. The structure was characterized by multiple-temperature X-ray diffraction and solid-state DFT computations. The material shows a geometric pattern of hydrogen bonding consistent with cooperativity between the intermolecular carboxylic acid dimer and intramolecular hydrogen bonds. The presence of proton disorder within this hydrogen-bond system, which would support such a cooperative model, was not fully ruled out by the initial X-ray studies. However, solid-state calculations on the three possible end-point tautomers indicate that the dominant crystallographically observed configuration is substantially lower in energy than the other tautomers (by at least 9 kJ mol(-1)), indicating that no disorder should be expected. It is therefore concluded that no disorder is observed either in the intra- or intermolecular hydrogen bonds of the title compound and that the cooperativity between the hydrogen bonds is not present within the temperature range studied.

Retrieval of crystallographically-derived molecular geometry information.

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.