Showing papers in "Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry in 2016"

The Cambridge Structural Database

Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

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

Abstract: 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.

On the effective ionic radii for ammonium

Abstract: A set of effective ionic radii corresponding to different coordination numbers (CNs) and compatible with the radii system by Shannon [Acta Cryst. (1976), A32, 751–767] has been derived for ammonium: 1.40 A (CN = IV), 1.48 A (CN = VI), 1.54 A (CN = VIII) and 1.67 A (CN = XII). The bond-valence parameters r0 = 2.3433 A and B = 0.262 A have been determined for ammonium–fluorine bonds.

Bond-length distributions for ions bonded to oxygen: alkali and alkaline-earth metals

Abstract: Bond-length distributions have been examined for 55 configurations of alkali-metal ions and 29 configurations of alkaline-earth-metal ions bonded to oxygen, for 4859 coordination polyhedra and 38 594 bond distances (alkali metals), and for 3038 coordination polyhedra and 24 487 bond distances (alkaline-earth metals). Bond lengths generally show a positively skewed Gaussian distribution that originates from the variation in Born repulsion and Coulomb attraction as a function of interatomic distance. The skewness and kurtosis of these distributions generally decrease with increasing coordination number of the central cation, a result of decreasing Born repulsion with increasing coordination number. We confirm the following minimum coordination numbers: [3]Li+, [3]Na+, [4]K+, [4]Rb+, [6]Cs+, [3]Be2+, [4]Mg2+, [6]Ca2+, [6]Sr2+ and [6]Ba2+, but note that some reported examples are the result of extensive dynamic and/or positional short-range disorder and are not ordered arrangements. Some distributions of bond lengths are distinctly multi-modal. This is commonly due to the occurrence of large numbers of structure refinements of a particular structure type in which a particular cation is always present, leading to an over-representation of a specific range of bond lengths. Outliers in the distributions of mean bond lengths are often associated with anomalous values of atomic displacement of the constituent cations and/or anions. For a sample of [6]Na+, the ratio Ueq(Na)/Ueq(bonded anions) is partially correlated with 〈[6]Na+—O2−〉 (R2 = 0.57), suggesting that the mean bond length is correlated with vibrational/displacement characteristics of the constituent ions for a fixed coordination number. Mean bond lengths also show a weak correlation with bond-length distortion from the mean value in general, although some coordination numbers show the widest variation in mean bond length for zero distortion, e.g. Li+ in [4]- and [6]-coordination, Na+ in [4]- and [6]-coordination. For alkali-metal and alkaline-earth-metal ions, there is a positive correlation between cation coordination number and the grand mean incident bond-valence sum at the central cation, the values varying from 0.84 v.u. for [5]K+ to 1.06 v.u. for [8]Li+, and from 1.76 v.u. for [7]Ba2+ to 2.10 v.u. for [12]Sr2+. Bond-valence arguments suggest coordination numbers higher than [12] for K+, Rb+, Cs+ and Ba2+.

How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures

Abstract: Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Moller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs.

High-Z' structures of organic molecules: their diversity and organizing principles.

Abstract: A list has been compiled of 284 well determined organic structures having more than four crystallographically independent molecules or formula units (i.e. Z' > 4). Another 22 structures were rejected because the space group or unit cell was probably misassigned; the rate for that type of error is then only 7%. The space-group frequencies are unusual; half the structures are in Sohncke groups, partly because the fraction of enantiopure structures of resolvable enantiomers is higher than for lower Z' structures. Careful investigation of the 284 structures has shown that they are very diverse; no simple classification can describe them all. Organizing principles have, however, been recognized for almost all of them. The most common features are simple modulations and hydrogen-bonded aggregates; only 14% of the structures have neither. In 50% of the structures n molecules are related by a pseudotranslation that would be a crystallographic translation but for small molecular displacements and rotations. In 70% of the structures there are aggregates (e.g. n-mers, columns or layers) held together by strong intermolecular interactions; those aggregates usually have approximate local symmetry. Because the n-fold modulations and the n-mers often have n 5 have several features that combine to give the high Z' value. The number of different molecular conformations is usually small, i.e. one or two in 84% of the structures. More exotic packing features, such as ordered faults and alternating layers of different types, are found in ca 30% of the structures. A very few structures are so complex that it is difficult to understand how the crystals could have formed.

Structural complexity and configurational entropy of crystals.

Abstract: Using a statistical approach, it is demonstrated that the complexity of a crystal structure measured as the Shannon information per atom [Krivovichev (2012). Acta Cryst. A68, 393-398] represents a negative contribution to the configurational entropy of a crystalline solid. This conclusion is in full accordance with the general agreement that information and entropy are reciprocal variables. It also agrees well with the understanding that complex structures possess lower entropies relative to their simpler counterparts. The obtained equation is consistent with the Landauer principle and points out that the information encoded in a crystal structure has a physical nature.

Crystal structure and phase transition of thermoelectric SnSe

Abstract: Tin selenide-based functional materials are extensively studied in the field of optoelectronic, photovoltaic and thermoelectric devices. Specifically, SnSe has been reported to have an ultrahigh thermoelectric figure of merit of 2.6 ± 0.3 in the high-temperature phase. Here we report the evolution of lattice constants, fractional coordinates, site occupancy factors and atomic displacement factors with temperature by means of high-resolution synchrotron powder X-ray diffraction measured from 100 to 855 K. The structure is shown to be cation defective with a Sn content of 0.982 (4). The anisotropy of the thermal parameters of Sn becomes more pronounced approaching the high-temperature phase transition (∼ 810 K). Anharmonic Gram–Charlier parameters have been refined, but data from single-crystal diffraction appear to be needed to firmly quantify anharmonic features. Based on modelling of the atomic displacement parameters the Debye temperature is found to be 175 (4) K. Conflicting reports concerning the different coordinate system settings in the low-temperature and high-temperature phases are discussed. It is also shown that the high-temperature Cmcm phase is not pseudo-tetragonal as commonly assumed.

Structure reinvestigation of α-, β- and γ-In2S3

Abstract: Semiconducting indium sulfide (In2S3) has recently attracted considerable attention as a buffer material in the field of thin film photovoltaics. Compared with this growing interest, however, detailed characterizations of the crystal structure of this material are rather scarce and controversial. In order to close this gap, we have carried out a reinvestigation of the crystal structure of this material with an in situ X-ray diffraction study as a function of temperature using monochromatic synchrotron radiation. For the purpose of this study, high quality polycrystalline In2S3 material with nominally stoichiometric composition was synthesized at high temperatures. We found three modifications of In2S3 in the temperature range between 300 and 1300 K, with structural phase transitions at temperatures of 717 K and above 1049 K. By Rietveld refinement we extracted the crystal structure data and the temperature coefficients of the lattice constants for all three phases, including a high-temperature trigonal γ-In2S3 modification.

Organic crystal polymorphism: a benchmark for dispersion-corrected mean-field electronic structure methods.

Abstract: We analyze the energy landscape of the sixth crystal structure prediction blind test targets with various first principles and semi-empirical quantum chemical methodologies. A new benchmark set of 59 crystal structures (termed POLY59) for testing quantum chemical methods based on the blind test target crystals is presented. We focus on different means to include London dispersion interactions within the density functional theory (DFT) framework. We show the impact of pairwise dispersion corrections like the semi-empirical D2 scheme, the Tkatchenko–Scheffler (TS) method, and the density-dependent dispersion correction dDsC. Recent methodological progress includes higher-order contributions in both the many-body and multipole expansions. We use the D3 correction with Axilrod–Teller–Muto type three-body contribution, the TS based many-body dispersion (MBD), and the nonlocal van der Waals density functional (vdW-DF2). The density functionals with D3 and MBD correction provide an energy ranking of the blind test polymorphs in excellent agreement with the experimentally found structures. As a computationally less demanding method, we test our recently presented minimal basis Hartree–Fock method (HF-3c) and a density functional tight-binding Hamiltonian (DFTB). Considering the speed-up of three to four orders of magnitudes, the energy ranking provided by the low-cost methods is very reasonable. We compare the computed geometries with the corresponding X-ray data where TPSS-D3 performs best. The importance of zero-point vibrational energy and thermal effects on crystal densities is highlighted.

Hexagonal RMnO3: a model system for two-dimensional triangular lattice antiferromagnets

Abstract: The hexagonal RMnO3(h-RMnO3) are multiferroic materials, which exhibit the coexistence of a magnetic order and ferroelectricity. Their distinction is in their geometry that both results in an unusual mechanism to break inversion symmetry and also produces a two-dimensional triangular lattice of Mn spins, which is subject to geometrical magnetic frustration due to the antiferromagnetic interactions between nearest-neighbor Mn ions. This unique combination makes the h-RMnO3 a model system to test ideas of spin-lattice coupling, particularly when both the improper ferroelectricity and the Mn trimerization that appears to determine the symmetry of the magnetic structure arise from the same structure distortion. In this review we demonstrate how the use of both neutron and X-ray diffraction and inelastic neutron scattering techniques have been essential to paint this comprehensive and coherent picture of h-RMnO3.

Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics

Abstract: Prediction and exploration of possible polymorphism in organic crystal compounds are of great importance for industries ranging from organic electronics to pharmaceuticals to high-energy materials. Here we apply our crystal structure prediction procedure and the enhanced molecular dynamics based sampling approach called the Crystal-Adiabatic Free Energy Dynamics (Crystal-AFED) method to benzene and naphthalene. Crystal-AFED allows the free energy landscape of structures to be explored efficiently at any desired temperature and pressure. For each system, we successfully predict the most stable crystal structures at atmospheric pressure and explore the relative Gibbs free energies of predicted polymorphs at high pressures. Using Crystal-AFED sampling, we find that mixed structures, which typically cannot be discovered by standard crystal structure prediction methods, are prevalent in the solid forms of these compounds at high pressure.

CH3NH3PbI3: precise structural consequences of water absorption at ambient conditions

Abstract: The crystal structure of the pristine (I) and aged (II) crystals of CH3NH3PbI3 (hereafter MAPbI3) hybrid organic–inorganic lead iodide has been studied at 293 K with high-precision single-crystal X-ray diffraction using a synchrotron light source. We show that (I) and (II) are characterized by an identical tetragonal unit cell but different space groups: I422 for (I) and P42212 for (II). Both space groups are subgroups of I4/mcm, which is widely used for MAPbI3. The main difference between (I) and (II) comes from the difference in hydrogen bonds between the MA+ cation and the PbI3 framework which is the direct consequence of H2O insertion in the aged crystal (II).

New polymorphs of an old drug: conformational and synthon polymorphism of 5-nitrofurazone

Abstract: Two new polymorphic forms of 5-nitrofurazone (5-nitro-2-furaldehyde semicarbazone) have been synthesized and structurally characterized by single-crystal and powder X-ray diffraction methods, vibrational spectroscopy (FT-IR and temperature Raman), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and Hirshfeld surface analysis. The compound crystallizes in three different polymorphic forms P21/a (polymorph α), P21 (polymorph β) and P21/c (polymorph γ), the crystal structures of two of which (polymorphs β and γ) represent new structure determinations. The solid-state molecular organization in the three crystal forms is analyzed and discussed in terms of molecular conformation, crystal packing and hydrogen-bonded networks. All three crystals are formed from trans geometrical isomers, but the molecular conformation of the α-polymorph is syn-anti-anti-anti, while that of β- and γ-polymorphs is syn-anti-syn-syn. As a consequence of this the hydrogen-bond donor and acceptor sites of the molecules are oriented differently, which in turn results in different hydrogen-bond connectivity and packing patterns.

Crystal structure prediction: are we there yet?

Abstract: This contribution comments on the advances of the latest Crystal Structure Prediction blind test and the challenges still lying ahead.

High-temperature single-crystal X-ray diffraction study of tetragonal and cubic perovskite-type PbTiO3 phases.

Abstract: A high-temperature single-crystal X-ray diffraction study of a synthetic PbTiO3 perovskite was carried out over the wide temperature range 298-928 K. A transition from a tetragonal (P4mm) to a cubic (Pm \bar 3 m) phase has been revealed near 753 K. In the non-centrosymmetric P4mm symmetry group, the difference in relative displacement between Pb and O along the c-axis is much larger than that between Ti and O. The Pb and Ti cations contribute sufficiently to polarization being shifted in the opposite direction compared with the shift of O atoms. Deviation from the linear changes in Debye-Waller factors and bonding distances in the tetragonal phases can be interpreted as a precursor phenomenon before the phase transition. Disturbance of the temperature factor Ueq for O is observed in the vicinity of the transition point, while Ueq values for Pb and Ti are continuously changing with increasing temperature. The O site includes the clear configurational disorder in the cubic phase. The polar local positional distortions remain in the cubic phase and are regarded as the cause of the paraelectricity. Estimated values of the Debye temperature ΘD for Pb and Ti are 154 and 467 K in the tetragonal phase and decrease 22% in the high-temperature phase. Effective potentials for Pb and Ti change significantly and become soft after the phase transition.

Charge distribution as a tool to investigate structural details. IV. A new route to heteroligand polyhedra

Abstract: A new route to apply the charge distribution (CHARDI) method to structures based on heteroligand coordination polyhedra is presented. The previous algorithm used scale factors computed in an iterative way based on the assumption (which turned out to be not always correct) that a real over-under bonding effect affects mainly the anionic charges of each single anion, without grossly modifying the total charge of each type of anion. The new, more general approach is not based on any a priori assumption but treats separately the homoligand sub-polyhedra and attributes to each type of atom a fraction of the charge of the atom coordinated to it, computed in a self-consistent iterative way. The distinction between the bonding and non-bonding contact is also redefined in terms of the mean fictive ionic radii (MEFIR), without the need of an empirical parameter, used in the previous algorithm. CHARDI equations are generalized in terms of the new approach and a series of examples is presented.

Hydrogen-substituted β-tricalcium phosphate synthesized in organic media

Abstract: β-Tricalcium phosphate (β-TCP) platelets synthesized in ethylene glycol offer interesting geometries for nano-structured composite bone substitutes but were never crystallographically analyzed. In this study, powder X-ray diffraction and Rietveld refinement revealed a discrepancy between the platelet structure and the known β-TCP crystal model. In contrast, a model featuring partial H for Ca substitution and the inversion of P1O4 tetrahedra, adopted from the whitlockite structure, allowed for a refinement with minimal misfits and was corroborated by HPO42− absorptions in Fourier-transform IR spectra. The Ca/P ratio converged to 1.443 ± 0.003 (n = 36), independently of synthesis conditions. As a quantitative verification, the platelets were thermally decomposed into hydrogen-free β-TCP and β-calcium pyrophosphate which resulted in a global Ca/P ratio in close agreement with the initial β-TCP Ca/P ratio (ΔCa/P = 0.003) and with the chemical composition measured by inductively coupled plasma (ΔCa/P = 0.003). These findings thus describe for the first time a hydrogen-substituted β-TCP structure, i.e. a Mg-free whitlockite, represented by the formula Ca21 − x(HPO4)2x(PO4)14 − 2x, where x = 0.80 ± 0.04, and may have implications for resorption properties of bone regenerative materials.

An optimized intermolecular force field for hydrogen‐bonded organic molecular crystals using atomic multipole electrostatics

Abstract: We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

Salt screening and characterization of ciprofloxacin.

Abstract: With the aim of improving the solubility of ciprofloxacin, polybasic organic acids were utilized to react with ciprofloxacin in different stoichiometric proportions. The use of the solvent drop grinding (SDG) method, as well as the solvent evaporation method, resulted in the crystalline salts ciprofloxacin/fumaric acid (1:1, 2:1), ciprofloxacin/maleic acid (1:1) and ciprofloxacin/citric acid (2:1). The solubilities of these salts in pure water (pH 7.0) were determined using high-performance liquid chromatography (HPLC) at 310 K, with the salts showing considerably greater solubility than ciprofloxacin itself and, interestingly, ciprofloxacin/fumaric acid (2:1) being more soluble than ciprofloxacin/fumaric acid (1:1). Intrigued by this phenomenon, we undertook a comparison of the crystal structures of the salts: the three-dimensional sandwich-like structure observed in the 2:1 salt indicates that the preferred stacking may be a factor in increasing the solubility of ciprofloxacin.

Source Function applied to experimental densities reveals subtle electron-delocalization effects and appraises their transferability properties in crystals.

Abstract: The Source Function (SF), introduced in 1998 by Richard Bader and Carlo Gatti, is succinctly reviewed and a number of paradigmatic applications to in vacuo and crystal systems are illustrated to exemplify how the SF may be used to discuss chemical bonding in both conventional and highly challenging cases. The SF enables the electron density to be seen at a point determined by source contributions from the atoms or a group of atoms of a system, and it is therefore well linked to the chemist's awareness that any local property and chemical behaviour is to some degree influenced by all the remaining parts of a system. The key and captivating feature of the SF is that its evaluation requires only knowledge of the electron density (ED) of a system, thereby enabling a comparison of ab initio and X-ray diffraction derived electron density properties on a common and rigorous basis. The capability of the SF to detect electron-delocalization effects and to quantify their degree of transferability is systematically explored in this paper through the analysis and comparison of experimentally X-ray derived Source Function patterns in benzene, naphthalene and (±)-8′-benzhydrylideneamino-1,1′-binaphthyl-2-ol (BAB) molecular crystals. It is shown that the SF tool recovers the characteristic SF percentage patterns caused by π-electron conjugation in the first two paradigmatic aromatic molecules in almost perfect quantitative agreement with those obtained from ab initio periodic calculations. Moreover, the effect of chemical substitution on the degree of transferability of such patterns to the benzene- and naphthalene-like moieties of BAB is neatly shown and quantified by the observed systematic deviations, relative to benzene and naphthalene, of only those SF contributions from the substituted C atoms. Finally, the capability of the SF to reveal electron-delocalization effects is challenged by using a promolecule density, rather than the proper quantum mechanical density, to determine the changes in SF patterns along the cyclohexene, 1,3-cyclohexadiene and benzene molecule series. It is shown that, differently from the proper quantum density, the promolecular density is unable to reproduce the SF trends anticipated by the increase of electron delocalization along the series, therefore ruling out the geometrical effect as being the only cause for the observed SF patterns changes.

Pyrite. A Natural History of Fool's Gold. By David Rickard. Oxford University Press, 2015. Hardback, XIX+297 pages, 4 colour plates. Price GBP 20.49. ISBN 9780190203672.

Abstract: HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Pyrite. A Natural History of Fool’s Gold . By David Rickard. Oxford University Press, 2015. Hardback, XIX+297 pages, 4 colour plates. Price GBP 20.49. ISBN 9780190203672. Massimo Nespolo

Variable-temperature single-crystal X-ray diffraction study of tetragonal and cubic perovskite-type barium titanate phases

Abstract: A variable-temperature single-crystal X-ray diffraction study of a synthetic BaTiO3 perovskite has been performed over the temperature range 298–778 K. A transition from a tetragonal (P4mm) to a cubic (Pm \overline 3 m) phase has been revealed near 413 K. In the non-centrosymmetric P4mm symmetry group, both Ti and O atoms are displaced along the c-axis in opposite directions with regard to the Ba position fixed at the origin, so that Ti4+ and Ba2+ cations occupy off-center positions in the TiO6 and BaO12 polyhedra, respectively. Smooth temperature-dependent changes of the atomic coordinates become discontinuous with the phase transition. Our observations imply that the cations remain off-center even in the high-temperature cubic phase. The temperature dependence of the mean-square displacements of Ti in the cubic phase includes a significant static component which means that Ti atoms are statistically distributed in the off-center positions.

Effect of packing motifs on the energy ranking and electronic properties of putative crystal structures of tricyano-1,4-dithiino[c]-isothiazole.

Abstract: We present an analysis of putative structures of tricyano-1,4-dithiino[c]-isothiazole (TCS3), generated within the sixth crystal structure prediction blind test. Typical packing motifs are identified and characterized in terms of distinct patterns of close contacts and regions of electrostatic and dispersion interactions. We find that different dispersion-inclusive density functional theory (DFT) methods systematically favor specific packing motifs, which may affect the outcome of crystal structure prediction efforts. The effect of crystal packing on the electronic and optical properties of TCS3 is investigated using many-body perturbation theory within the GW approximation and the Bethe–Salpeter equation (BSE). We find that a structure with Pna21 symmetry and a bilayer packing motif exhibits intermolecular bonding patterns reminiscent of π–π stacking and has markedly different electronic and optical properties than the experimentally observed P21/n structure with a cyclic dimer motif, including a narrower band gap, enhanced band dispersion and broader optical absorption. The Pna21 bilayer structure is close in energy to the observed structure and may be feasible to grow.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2‐nitroimidazole: an experimental and theoretical study

Abstract: An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen-Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density rho(bcp)(r) and the Laplacian of electron density del(2) rho(bcp)(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed using CRYSTAL09.

New multi-component solid forms of anti-cancer drug Erlotinib: role of auxiliary interactions in determining a preferred conformation.

Abstract: Erlotinib is a BCS (biopharmaceutical classification system) class II drug used for the treatment of non-small cell lung cancer. There is an urgent need to obtain new solid forms of higher solubility to improve the bioavailability of the API (active pharmaceutical ingredient). In this context, cocrystals with urea, succinic acid, and glutaric acid and salts with maleic acid, adipic acid, and saccharin were prepared via wet granulation and solution crystallizations. Crystal structures of the free base (Z' = 2), cocrystals of erlotinib-urea (1: 1), erlotinib-succinic acid monohydrate (1: 1: 1), erlotinib-glutaric acid monohydrate (1: 1: 1) and salts of erlotinib-adipic acid adipate (1: 0.5: 0.5) are determined and their hydrogen-bonding patterns are analyzed. Self recognition via the (amine) N-H center dot center dot center dot N (pyridine) hydrogen bond between the API molecules is replaced by several heterosynthons such as acid-pyridine, amide-pyridine and carboxylate-pyridinium in the new binary systems. Auxiliary interactions play an important role in determining the conformation of the API in the crystal. FT-IR spectroscopy is used to distinguish between the salts and cocrystals in the new multi-component systems. The new solid forms are characterized by powder X-ray diffraction (PXRD) and differential scanning calorimetry (DSC) to confirm their unique phase identity.

Silver(I) coordination polymers assembled from flexible cyclotriphosphazene ligand: structures, topologies and investigation of the counteranion effects

Abstract: The reactions of a flexible ligand hexakis(3-pyridyloxy)cyclotriphosphazene (HPCP) with a variety of silver(I) salts (AgX; X = NO3(-), PF6(-), ClO4(-), CH3PhSO3(-), BF4(-) and CF3SO3(-)) afforded six silver(I) coordination polymers, namely {[Ag2(HPCP)]·(NO3)2·H2O}n (1), {[Ag2(HPCP)(CH3CN)]·(PF6)2}n (2), {[Ag2(HPCP)(CH3CN)]·(ClO4)2}n (3), [Ag3(HPCP)(CH3PhSO3)3]n (4), [Ag2(HPCP)(CH3CN)(BF4)2]n (5) and {[Ag(HPCP)]·(CF3SO3)}n (6). All of the isolated crystalline compounds were structurally determined by X-ray crystallography. Changing the counteranions in the reactions, which were conducted under similar conditions of M/L ratio (1:1), temperature and solvent, resulted in structures with different types of topologies. In complexes (1)-(6), the ligand HPCP shows different coordination modes with Ag(I) ions giving two-dimensional layered structures and three-dimensional frameworks with different topologies. Complex (1) displays a new three-dimensional framework adopting a (3,3,6)-connected 3-nodal net with point symbol {4.6(2)}2{4(2).6(10).8(3)}. Complexes (2) and (3) are isomorphous and have a two-dimensional layered structure showing the same 3,6L60 topology with point symbol {4.2(6)}2{4(8).6(6).8}. Complex (4) is a two-dimensional structure incorporating short Ag...Ag argentophilic interactions and has a uninodal 4-connected sql/Shubnikov tetragonal plane net with {4(4).6(2)} topology. Complex (5) exhibits a novel three-dimensional framework and more suprisingly contains twofold interpenetrated honeycomb-like networks, in which the single net has a trinodal (2,3,5)-connected 3-nodal net with point symbol {6(3).8(6).12}{6(3)}{8}. Complex (6) crystallizes in a trigonal crystal system with the space group R\bar 3 and possesses a three-dimensional polymeric structure showing a binodal (4,6)-connected fsh net with the point symbol (4(3).6(3))2.(4(6).6(6).8(3)). The effect of the counteranions on the formation of coordination polymers is discussed in this study.

Electron density, disorder and polymorphism:high-resolution diffraction studies of the highly polymorphic neuralgic drug carbamazepine

Abstract: Analysis of neutron and high-resolution X-ray diffraction data on form (III) of carbamazepine at 100 K using the atoms in molecules (AIM) topological approach afforded excellent agreement between the experimental results and theoretical densities from the optimized gas-phase structure and from multipole modelling of static theoretical structure factors. The charge density analysis provides experimental confirmation of the partially localized π-bonding suggested by the conventional structural formula, but the evidence for any significant C—N π bonding is not strong. Hirshfeld atom refinement (HAR) gives H atom positional and anisotropic displacement parameters that agree very well with the neutron parameters. X-ray and neutron diffraction data on the dihydrate of carbemazepine strongly indicate a disordered orthorhombic crystal structure in the space group Cmca, rather than a monoclinic crystal structure in space group P21/c. This disorder in the dihydrate structure has implications for both experimental and theoretical studies of polymorphism.

Generation of crystal structures using known crystal structures as analogues

Abstract: This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach.

Why direct and post-refinement determinations of absolute structure may give different results

Abstract: Direct determination of the Flack parameter as part of the structure refinement procedure usually gives different, though similar, values to post-refinement methods. The source of this discrepancy has been probed by analysing a range of data sets taken from the recent literature. Most significantly, it was observed that the directly refined Flack (x) parameter and its standard uncertainty are usually not much influenced by changes in the refinement weighting schemes, but if they are then there are probably problems with the data or model. Post-refinement analyses give Flack parameters strongly influenced by the choice of weights. Weights derived from those used in the main least squares lead to post-refinement estimates of the Flack parameters and their standard uncertainties very similar to those obtained by direct refinement. Weights derived from the variances of the observed structure amplitudes are more appropriate and often yield post-refinement Flack parameters similar to those from direct refinement, but always with lower standard uncertainties. Substantial disagreement between direct and post-refinement determinations are strongly indicative of problems with the data, which may be difficult to identify. Examples drawn from 28 structure determinations are provided showing a range of different underlying problems. It seems likely that post-refinement methods taking into account the slope of the normal probability plot are currently the most robust estimators of absolute structure and should be reported along with the directly refined values.