Synthesis, structure and Hirshfeld surface analysis of 2-oxo-2H-chromen-6-yl 4-tert-butyl-benzoate: work carried out as part of the AFRAMED project.

In the title compound, C20H18O4, the dihedral angle between the 2H-chromen-2-one ring system and the phenyl ring is 89.12 (5)°. In the crystal, the mol-ecules are connected through C-H⋯O hydrogen bonds to generate [010] double chains that are reinforced by weak aromatic π-π stacking inter-actions. The unit-cell packing can be described as a tilted herringbone motif. The H⋯H, H⋯O/O⋯H, H⋯C/C⋯H and C⋯C contacts contribute 46.7, 24.2, 16.7 and 7.6%, respectively, to its Hirshfeld surface.

Synthesis, crystal structure and phase transitions of novel hybrid perovskite: bis(1,2-diaminopropane) di-µ-chloro-bis[diaquadichloromanganate(II)] dichloride.

Single crystals of bis(1,2-diaminepropane) di-µ-chloro-bis[diaquadichloromanganate(II)] dichloride have been prepared by evaporation from ethanoic solution. The triclinic X-ray crystal structure is built as layers of centrosymmetric dimers of [Mn(Cl)4(H2O)2]2- octahedra and 1,2-diaminopropane. The inorganic part consists of Mn octahedra sharing one edge and distributed in the basal ac plane along the a direction. These doubly negative charged layers are separated along the b axis by a positively charged diamine propane layer. One Cl- anion contributes to the electroneutrality of the crystal interacting with both inorganic - through a hydrogen bond network to the two water molecules coordinated to Mn - and organic layers via the NH3+ ammonium group. Differential scanning calorimetry shows two endothermic main peaks at T = 366 K and T = 375 K related to the release of the water molecules. The resulting dehydrated material is C-centered monoclinic as shown by powder X-ray diffraction.

Spin-resolved atomic orbital model refinement for combined charge and spin density analysis: application to the YTiO3 perovskite.

A new crystallographic method is proposed in order to refine a spin-resolved atomic orbital model against X-ray and polarized neutron diffraction data. This atomic orbital model is applied to the YTiO3 perovskite crystal, where orbital ordering has previously been observed by several techniques: X-ray diffraction, polarized neutron diffraction and nuclear magnetic resonance. This method gives the radial extension, orientation and population of outer atomic orbitals for each atom. The interaction term between Ti3+, Y3+ cations and O2- ligands has been estimated. The refinement statistics obtained by means of the orbital method are compared with those obtained by the multipole model previously published.

Crystal structure of di-ammonium bis-[tris-(oxamide dioxime-κ2 N,N')nickel(II)] bis-[tris-(oxalato-κ2 O,O')chromate(III)] 6.76-hydrate.

The asymmetric unit of the title compound, (NH4)2[Ni(C2H6N4O2)3]2[Cr(C2O4)3]2·6.76H2O, comprises two NH4 + cations, two [Ni(C2H6N4O2)3]2+ cations and two [Cr(C2O4)3]3- anions, as well as eight water mol-ecules of crystallization of which only one is fully occupied. In the cationic and anionic complexes, the central atoms (NiII and CrIII) are each surrounded by three bidentate ligands (N-chelating oxamide dioxime and O-chelating oxalate, respectively), resulting in distorted octa-hedral coordination spheres. In the crystal, O-H⋯O hydrogen bonds between the oxamide dioxime ligands as donor groups and the oxalate ligands as acceptor groups alternately connect the cationic and anionic complexes into infinite pillars extending parallel to [100]. Moreover, N-H⋯O hydrogen bonds between the same ligands connect neighboring pillars, thus delineating channels that accommodate the charge-balancing NH4 + cations as well as the water mol-ecules of crystallization. Although the H atoms could not be localized for these two species, the corresponding N⋯O and O⋯O distances indicate hydrogen bonds of medium strength.

Hexa-aqua-nickel(II) bis-[tri-aqua-µ3-oxalato-di-µ-oxalato-bariumchromate(III)] tetra-hydrate.

The title compound, [Ni(H2O)6][BaCr(C2O4)3(H2O)3]2·4H2O, was obtained in the form of single crystals from the slow evaporation of an aqueous mixture of {Ba6(H2O)17[Cr(C2O4)3]4}·7H2O and NiSO4·6H2O in the molar ratio 1:4. Its structure is made up of corrugated anionic (101) layers of formula [BaCr(C2O4)3(H2O)3] n n - that leave voids accommodating the charge-compensating cations, [Ni(H2O)6]2+ (point group symmetry ), as well as the water mol-ecules of crystallization. The anionic layers are built from the connection of barium and chromium atoms through bridging oxalate ligands. The CrIII atom is hexa-coordinated by O atoms of three oxalate ligands while the BaII atom is tenfold coordinated by three O atoms of water mol-ecules and seven O atoms of four oxalate ligands. Each NiII atom sits on an inversion center and is coordinated by six water mol-ecules. One of the uncoordinated water mol-ecules is disordered over two sites, with a refined occupancy ratio of 0.51 (5):0.49 (5). In the crystal, extensive O-H⋯O hydrogen-bonding inter-actions link the anionic layers, the charge-balancing cations as well as the water mol-ecules of crystallization into a three-dimensional supra-molecular network.

Crystal structure of a new phen-yl(morpholino)methane-thione derivative: 4-[(morpholin-4-yl)carbothioyl]benzoic acid.

4-[(Morpholin-4-yl)carbothioyl]benzoic acid, C12H13NO3S, a novel phen-yl(morpholino)methane-thione derivative, crystallizes in the monoclinic space group P21/n. The morpholine ring adopts a chair conformation and the carb-oxy-lic acid group is bent out slightly from the benzene ring mean plane. The mol-ecular geometry of the carb-oxy-lic group is characterized by similar C-O bond lengths [1.266 (2) and 1.268 (2) Å] as the carboxyl-ate H atom is disordered over two positions. This mol-ecular arrangement leads to the formation of dimers through strong and centrosymmetric low barrier O-H⋯O hydrogen bonds between the carb-oxy-lic groups. In addition to these inter-molecular inter-actions, the crystal packing consists of two different mol-ecular sheets with an angle between their mean planes of 64.4 (2)°. The cohesion between the different layers is ensured by C-H⋯S and C-H⋯O inter-actions.

Spin resolved electron density study of YTiO3 in its ferromagnetic phase: signature of orbital ordering.

The present work reports on the charge and spin density modelling of YTiO3 in its ferromagnetic state (T C = 27 K). Accurate polarized neutron diffraction and high-resolution X-ray diffraction (XRD) experiments were carried out on a single crystal at the ORPHÉE reactor (LLB) and SPRING8 synchrotron source. The experimental data are modelled by the spin resolved pseudo-atomic multipolar model (Deutsch et al., 2012 ▸). The refinement strategy is discussed and the result of this electron density modelling is compared with that from XRD measured at 100 K and with density functional theory calculations. The results show that the spin and charge densities around the Ti atom have lobes directed away from the O atoms, confirming the filling of the t 2g orbitals of the Ti atom. The d xy orbital is less populated than d xz and d yz , which is a sign of a partial lift of degeneracy of the t 2g orbitals. This study confirms the orbital ordering at low temperature (20 K), which is already present in the paramagnetic state above the ferromagnetic transition (100 K).

Exploring the simultaneous σ-hole/π-hole bonding characteristics of a Br⋯π interaction in an ebselen derivative via experimental and theoretical electron-density analysis.

In this study, the nature and characteristics of a short Br⋯π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br⋯π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br⋯π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).

Boron triel bonding: a weak electrostatic interaction lacking electron-density descriptors.

In an effort to describe π-hole interactions, we undertook accurate high-resolution X-ray diffraction analyses of single crystals of 1,4-dinitrobenzene, a co-crystal of cis-tartaric acid and bis-pyridine N-oxide and the hydrochloride of B-4-pyridinylboronic acid. We selected these three compounds owing to the π-hole accessibility features that the sp2 hybridized B, C and N atoms provide, thus allowing us to compare the fundamental characteristics of π-hole interactions using Bader's Atom in Molecules (AIM) theory. This particular study required extremely accurate experimental diffraction data, because the interaction of interest is weak. As shown by the experimental charge density maps of the -YO2 (Y = B, C, N) units, we assign the depletion of electron-density present in the central boron, carbon and nitrogen atoms (electrophilic π-holes) as the main origin for the establishment of intermolecular Lewis acid-Lewis base attractive interaction with complementary electron-rich regions. Unexpectedly, the Bader's analyses of both experimentally and theoretically calculated charge distribution maps for the solid involving the - BO2H2 group do not show the presence of bond paths, neither of the bond critical points, between the interacting electron rich sites and the boron or carbon atoms featuring the electron hole. In contrast, these topological descriptors of chemical interactions for the AIM theory were easily located in the solid-state structures of the compounds involving the carboxylic and the nitro groups.

Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO3 crystal along the Ti-O1-Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

A method to estimate statistical errors of properties derived from charge-density modelling.

Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance-covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Šresolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.

When combined X-ray and polarized neutron diffraction data challenge high-level calculations: spin-resolved electron density of an organic radical.

Joint refinement of X-ray and polarized neutron diffraction data has been carried out in order to determine charge and spin density distributions simultaneously in the nitronyl nitroxide (NN) free radical Nit(SMe)Ph. For comparison purposes, density functional theory (DFT) and complete active-space self-consistent field (CASSCF) theoretical calculations were also performed. Experimentally derived charge and spin densities show significant differences between the two NO groups of the NN function that are not observed from DFT theoretical calculations. On the contrary, CASSCF calculations exhibit the same fine details as observed in spin-resolved joint refinement and a clear asymmetry between the two NO groups.

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model.

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

Modelling the experimental electron density: only the synergy of various approaches can tackle the new challenges.

Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.

On atom-atom 'short contact' bonding interactions in crystals.

Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom-atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.

Isomorphism and solid solution as shown by an accurate high-resolution diffraction experiment.

High-resolution crystal structure determination and spherical and multipolar refinement enabled an organic solid solution of 1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile and 5-bromo-1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole to be found, which would not normally be revealed using only standard resolution data (ca 0.8 Å), as the disordered part is only visible at high resolution. Therefore, this new structure would have been reported as just another polymorphic form, even more reasonably as isostructural with other derivatives. To the best of our knowledge this is the first example of organic solid solution modelled via charge density Hansen-Coppens formalism and analysed by means of quantum theory of atoms in molecules (QTAIM) theory.

XPAD X-ray hybrid pixel detector for charge density quality diffracted intensities on laboratory equipment.

The new generation of X-ray detectors, the hybrid pixel area detectors or `pixel detectors', is based on direct detection and single-photon counting processes. A large linearity range, high dynamic and extremely low noise leading to an unprecedented high signal-to-noise ratio, fast readout time (high frame rates) and an electronic shutter are among their intrinsic characteristics which render them very attractive. First used on synchrotron beamlines, these detectors are also promising in the laboratory, in particular for pump-probe or quasi-static experiments and accurate electron density measurements, as explained in this paper. An original laboratory diffractometer made from a Nonius Mach3 goniometer equipped with an Incoatec Mo microsource and an XPAD pixel area detector has been developed at the CRM2 laboratory. Mo Kα accurate charge density quality data up to 1.21 Å(-1) resolution have been collected on a sodium nitroprusside crystal using this home-made diffractometer. Data quality for charge density analysis based on multipolar modelling are discussed in this paper. Deformation electron densities are compared to those already published (based on data collected with CCD APEXII and CAD4 diffractometers).

Two-dimensionally stacked heterometallic layers hosting a discrete chair dodecameric ring of water clusters: synthesis and structural study.

The stacked two-dimensional supramolecular compound catena-{Co(amp)3Cr(ox)3·6H2O} (amp = 2-picolylamine, ox = oxalate) has been synthesized from the bimolecular approach using hydrogen bonds. It is built from layers in which both Co(amp)(3+) (D) and Cr(ox)(3-) (A) ions are bonded in a repeating DADADA… pattern along the a and c axes by multiple hydrogen bonds. These layers host a well resolved R12 dodecameric discrete ring of water clusters built by six independent molecules located around the 2c centrosymmetric Wyckoff positions of the P21/n space group in which the compound crystallizes. These clusters are ranged along the [001] direction, occupy 733.5 Å(3) (22.0%) of the unit cell and have a chair conformation via 12 hydrogen bonds. The water molecules of the cluster are linked with stronger hydrogen bonds than those between the cluster and its host, which explains the single continuous step of the dehydration process of the compound.

Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole.

The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365-378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called 'shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.