Kryptoracemic compound hunting and frequency in the Cambridge Structural Database

Herein, a novel mechano-responsive luminescent (MRL) material based on crystal-to-crystal phase transitions between crystals of a chiral and those of a centrosymmetric space group, accompanied by a change of emission properties, is described. Initially, a gold complex containing a biphenyl moiety, which exhibits an achiral structure in solution, afforded an orange-emitting amorphous phase together with a viscous isotropic oil after evaporation of the solvent. Upon pricking, the orange-emitting oil spontaneously crystallized either in a centrosymmetric or in a chiral space group while simultaneously changing the emission properties. Remarkably, grinding the chiral crystals induced a solid-state phase transition to the achiral crystals under concomitant changes of the emission properties.

The molten reaction of 2-naphthol, 4-(aminomethyl)pyridine, and 4-pyridinecarboxaldehyde at about 180 degrees C yields trans-2,3-dihydro-2,3-di(4'-pyridyl)benzo[e]indole (1) which possesses two chiral centers, rather than an expected Betti-type reaction product with only one chiral carbon center. The same reactions, using 3-pyridinecarboxaldehyde, 4-cyanobenzaldehyde, or 3- cyanobenzaldehyde instead of 4-pyridinecarboxaldehyde produce the related compounds trans-2,3-dihydro-2-(4'-pyridyl)-3-(3"-pyridyl)benzo[e]indole (2), trans-2,3-dihydro-2-(4'-pyridyl)-3-(4"-cyanophenyl)benzo[e]indole (3), and trans-2,3-dihydro-2-(4'-pyridyl)-3-(3"-cyanophenyl)benzo[e]indole (4), respectively. This reaction proceeds with a high degree of stereoselectivity with a trans/cis ratio of about 98:2 at elevated temperature. Compounds 1, 2, and 4 crystallize in a noncentrosymmetric space group (Pca2(1), Pca2(1), and Cc), while compound 3 has a chiral space group (P2(1)). These successfully acentric packing arrangements are probably due to the molecule bearing both two chiral centers and potential hydrogen-bonding groups. Furthermore, the reaction of racemic 6-hydroxy-2'-methyl-2-naphthaleneacetic acid with ethyl-2-cyano-1-(4'-pyridyl)acrylic acetate in the presence of piperidine gives 1-pyridyl-2-ethoxycarbonyl-3-amino-1H-naphtho[2,1-b]pyran-2'-methylacetic acid (5), which likewise crystallizes in a chiral space group. All of compounds are second harmonic generation (SHG) active, and have a very strong SHG response approximately about 8.0, 5.0, 12.0, 6.0, and 1.4 (for 1-5 compounds) times that of urea. Ferroelectric property measurements indicate that compounds 1, 2, 4, and 5 may display ferroelectric behavior.

Organometallic antimony(V) complexes were prepared as model compounds to better understand the interactions of chiral chelating diols with this metalloid. These complexes feature three aryl groups (meta-xylyl or para-tolyl) and a bidentate trans-2,3-butanediolate. The meta-xylyl and para-tolyl complexes of either enantiomerically pure 2R,3R-butanediolate or 2S,3S-butanediolate (compounds 1-4) crystallized in Sohncke space groups, as expected. In each case, though, pseudoinversion centers were present that mimic higher-symmetry space groups through global pseudosymmetry. We hypothesized that the crystallization of 1:1 mixtures of the enantiomeric complexes would produce crystals in the centrosymmetric space group approximated by the pseudosymmetry. The enantiomerically pure meta-xylyl complexes each crystallized in space group P1 (approximating P1̅), and the racemic compound did indeed crystallize in P1̅. The enantiomerically pure para-tolyl complexes each crystallized in space group P21 (approximating P21/c), but the racemic compound crystallized in P1̅. Although the enantiomerically pure and racemic compounds are not isostructural, there are similarities in their 3D structures that are analyzed.

A Gold Quartet Framework with Reversible Anisotropic Structural Transformation Accompanied by Luminescence Response

Crystals and crystal structures

Chirality transfer, induction, and circularly polarized luminescence (CPL) using supramolecular hosts, such as macrocycles and cages, have been explored for wide-ranging applications in chiral reco...

Two new coordination polymers with the same topological structure, [Zn(L)]_2n·n(H₂O) (<b>1</b>) and [Co(L)]_2n·n(H₂O) (<b>2</b>) (H₂L = 5-(pyridin-2-ylmethoxy)-isophthalic acid), have been hydrothermally synthesized by reactions of metal salts and H₂L. Single crystal X-ray analyses reveal that <b>1</b> and <b>2</b> are isostructural and crystallize in orthorhombic, chiral <i>P</i>2₁2₁2 space group. These compounds feature 2D undulated layer structures with (3,6)-connected <b>kgd</b> topology, which further extended into a 3D suparmolecular framework <i>via</i> intermolecular hydrogen bonds. In addition, the luminescent properties of <b>1</b> and <b>2</b> and the magnetic property of <b>2</b> were also investigated.

Supramolecular assembly based on a series of meso-tetrakis( p-methoxyphenyl)porphrin complexes

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

The syntheses, crystal structures, and magnetic properties of three novel cyano-bridged bimetallic assemblies, [Ni(bpm)(2)](3)[Co(CN)(6)](2)x3.5H(2)O (1), [Co(bpm)(2)][Fe(CN)(5)NO]x2H(2)O (2), and [Co(bpm)(2)][Ni(CN)(4)] (3) (bpm = bis(1-pyrazolyl)methane), are reported. Complex 1 crystallizes in the tetragonal space group P4(3)2(1)2 with a = 12.800(5) A, b = 12.800(5) A, c = 42.80(3) A, V = 7012(6) A(3), and Z = 8. Complex 2 crystallizes in the chiral trigonal space group P3(2)21 with a = 11.9961(19) A, b = 11.9961(19) A, c = 16.062(5) A, gamma = 120 degrees , V = 2001.7(8) A(3), and Z = 3. Complex 1 is a trigonal bipyramidal complex in which three [Ni(bpm)(2)](2+) units are situated in the equatorial plane and are connected to the two apical [Co(CN)(6)](3)(-) units via three N ends of the cyanide groups. Complex 2 possesses a triangular left-handed helical chain structure composed of [Co(bpm)(2)](2+) linked by [Fe(CN)(5)NO](2)(-); the shortest intramolecular Co...Fe distance is 5.162 A. To the best of our knowledge, this is the first observation of a heteronuclear helical chain structure based on pentacyanonitrosylferrate(II). The structure of complex 3 is roughly determined by X-ray crystallograhy analysis to be a 1D zigzag chain. These structure variations, from a discrete cluster to a 1D helical chain and a 1D zigzag chain, rely on the semirigidity of the capping ligand bpm. Magnetic susceptibility measurements indicate that complex 1 has an intramolecular ferromagnetic interaction (J = 4.06 cm(-)(1)) between the nickel(II) ions; this is further confirmed by the magnetization measurements. In complexes 2 and 3, the cobalt(II) ions are located in a moderately strong field.

Pyruvate kinase is a key regulatory enzyme involved in the glycolytic pathway. The crystal structure of Escherichia coli type I pyruvate kinase was first solved in 1995 at 2.5 Å resolution. However, the space group was ambiguous, being either primitive orthorhombic (P2(1)2(1)2(1)) or C-centred orthorhombic (C222(1)). Here, the structure determination and refinement of E. coli type I pyruvate kinase to 2.28 Å resolution are presented. Using the same crystallization conditions as reported previously, the enzyme was found to crystallize in space group P2(1). Determination of the space group was complicated owing to anisotropic data, pseudo-translational noncrystallographic symmetry and the pseudo-merohedrally twinned nature of the crystal, which was found to have very close to 50% twinning, leading to apparent orthorhombic symmetry and absences that were not inconsistent with P2(1)2(1)2(1). The unit cell contained two tetramers in the asymmetric unit (3720 residues) and, when compared with the orthorhombic structure, virtually all of the residues could be easily modelled into the density. Averaging of reflections into the lower symmetry space group with twinning provided tidier electron density that allowed ∼30 missing residues of the lid domain to be modelled for the first time. Moreover, residues in a flexible loop could be modelled and sulfate molecules are found in the allosteric binding domain, identifying the pocket that binds the allosteric activator fructose 1,6-bisphosphate in this isozyme for the first time. Lastly, we note the pedagogical benefits of difficult structures to emerging crystallographers.

Black box' approaches to the prediction of properties are greatly hindered by ambiguities in data representation [1].A crystal structure can be represented by infinitely many different bases and motifs.Crystal Structure Prediction produces numerous near-duplicates among millions of simulated crystals, obtained as slightly different approximations of the same local energy minimum, which must be distinguished from genuinely different structures [2].Since crystal structures are determined in a rigid form, their strongest equivalence is rigid motion or isometry also including reflections.Their classification up to isometry requires invariants and metrics that are continuous under perturbations because any conventional or reduced basis may double in size under small perturbations.Density functions [3], the isoset (a complete invariant of periodic structures) [4], Average Minimum Distances (AMD) open up the 'black box' of crystallographic data with unambiguous representations of periodic structures [5].The simplest Gaussian regression on AMD invariants [6] achieved the state-of-the-art Mean Absolute Error (less than 5kJ/mole, 0.05eV/atom) on 5679 crystals [2].Pointwise Distance Distributions (PDD) are stronger invariants, which can be continuously compared by the Earth Mover's Distance.This distance was used for visualising the Inorganic Crystal Structure Database [7].More than 200 billion pairwise comparisons between all 660K+ periodic crystals (full 3D structure; no disorder) in the Cambridge Structural Database (CSD) was completed over two days on a modest desktop PC.PDD computations detected five pairs of entries that have identical geometry but differ by one pair of atoms, for example, Cd<->Mn in HIFCAB vs JEPLIA [8, section 7].Since these coincidences seem physically impossible, five journals are now investigating the integrity of publications based on these duplicates.These experiments justify the Crystal Isometry Principle, which states that any periodic crystal is uniquely determined by its geometric structure.Indeed, replacing any atom with a different one inevitably perturbs distances between neighbours.Then all periodic crystals live in a common Crystal Isometry Space (CRISP), so that Mendeleev's periodic table representing individual elements, categorised by atomic number and group, can be extended into a continuous space for all solid crystalline materials.For instance, diamond and graphite, both consisting purely of carbon, have different locations in CRISP.In the case of 2-dimensional lattices [9], the first map of CRISP shows that among all real crystals in the CSD about 45% of 2-dimensional lattices are oblique and nicely fill the expected continuous space [10] except towards the point representing very thin long cells.

In order to identify all pairs of polymorphs in the Cambridge Structural Database (CSD), a method was devised to automatically compare two crystal structures. The comparison is based on simulated powder diffraction patterns, but with special provisions to deal with differences in unit-cell volumes caused by temperature or pressure. Among the 325,000 crystal structures in the Cambridge Structural Database, 35,000 pairs of crystal structures of the same chemical compound were identified and compared. A total of 7300 pairs of polymorphs were identified, of which 154 previously were unknown.

Machine learning was employed on the experimental crystal structures of the Cambridge Structural Database (CSD) to derive an intermolecular force field for all available types of atoms (general force field). The obtained pairwise interatomic potentials of the general force field allow for the fast and accurate calculation of intermolecular Gibbs energy. The approach is based on three postulates regarding Gibbs energy: the lattice energy must be below zero, the crystal structure must be a local minimum, and, if available, the experimental and the calculated lattice energy must coincide. The parametrized general force field was then validated regarding these three conditions. First, the experimental lattice energy was compared with the calculated energies. The observed errors were found to be in the order of experimental errors. Second, Gibbs lattice energy was calculated for all structures available in the CSD. Their energy values were found to be below zero in 99.86% of the cases. Finally, 500 random structures were minimized, and the change in density and energy was examined. The mean error in the case of density was below 4.06%, and for energy it was below 5.7%. The obtained general force field calculated Gibbs lattice energies of 259 041 known crystal structures within a few hours. Since Gibbs energy defines the reaction energy, the calculated energy can be used to predict chemical-physical properties of crystals, for instance, the formation of co-crystals, polymorph stability and solubility.

Using the parameters of Voronoi-Dirichlet (VD) polyhedra the authors have verified the maximum space-filling principle in substructures constructed of actinide atoms (from thorium to einsteinium) in all crystal structures from the Inorganic Crystal Structure Database (ICSD) and Cambridge Structural Database (CSD). It is shown that most of the actinide atoms in such substructures are surrounded by 14 or 12 neighboring atoms. It was discovered that U substructures with greater than or equal to 20 crystallographically independent U atoms in the unit cell feature 15-faceted VD polyhedra as the most common type. Analogous unimodal distributions of VD polyhedra with maxima at 15 faces are observed for F and H substructures and the model system `ideal gas', which has no order in the arrangement of atoms. This similarity allows one to assume that substructures of crystal structures with greater than or equal to 20 crystallographically independent atoms in the unit cell do not possess short-range (local) order in the mutual arrangement of atoms, but feature long-range order (translational symmetry). Thus, crystalline compounds with such substructures can formally be regarded as `antiliquid', that is the antipode of a liquid, whose structure possesses short-range order but lacks translational symmetry.