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Acta Crystallographica Section B



Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials publishes scientific articles related to the structural science of compounds and materials in the widest sense. Knowledge of the arrangements of atoms, including their



Published: 2016-08-01

 






Crystal structure prediction: are we there yet?

2016-08-01

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



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

2016-08-01

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.



Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods

2016-07-16

A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.



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

2016-07-16

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%.



Crystal structure prediction of rigid molecules

2016-08-01

A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r6 dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.



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

2016-08-01

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.



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

2016-07-16

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 Möller–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.



Generation of crystal structures using known crystal structures as analogues

2016-07-16

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.



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

2016-08-01

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.



Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts

2016-07-16

The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol−1 of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of a Z′ = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.



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

2016-08-01

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.



An insight into real and average structure from diffuse X-ray scattering – a case study

2016-08-01

Two-dimensional diffuse X-ray scattering from an organic salt [N-(3-(2,6-dimethylanilino)-1-methylbut-2-enylidene)-2,6-dimethylanilinium chloride, C21H27N2+Cl−] was interpreted with the help of an analytical model of diffuse scattering. An analysis of the relationship between symmetry and diffuse scattering for the studied system has been undertaken. The symmetry of the system explains the extinction pattern, taking the form of curves, on the diffuse scattering planes. We have also tested the relationship between the average structure model and scattering intensities. Two models, differing in their representation of overlapping atoms, were used. In the case of diffuse scattering the difference between resulting intensities is immense, while for the Bragg intensities it is much smaller. This sensitivity of diffuse scattering could potentially be used to improve the description of the average structure.



Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules

2016-08-01

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.



Growth, morphology, structure and characterization of l-histidinium dihydrogen arsenate orthoarsenic acid single crystal

2016-08-01

l-Histidinium dihydrogen arsenate orthoarsenic acid (LHAS) crystals were grown by the slow evaporation method. Single-crystal X-ray diffraction confirms monoclinic structure. The growth rates of various planes of LHAS crystals were estimated by morphological study. Hirshfeld surface and fingerprint plots were analyzed to investigate the intermolecular interactions at 0.002 a.u. present in the crystal structure. The functional groups and phase behavior of the compound are studied by FTIR spectroscopy and differential scanning calorimetry (DSC). A ferroelectric to paraelectric phase transition at 307 K was observed in dielectric studies. The piezoelectric charge coefficients of the grown crystal were found to be 2 pC/N. The values of coercive field (Ec), remnant polarization (Pr) and spontaneous polarization (Ps) in the hysteresis loop are found to be 5.236 kV cm−1, 0.654 µC cm−2 and 2.841 µC cm−2, respectively. Piezoelectricity and ferroelectricity are reported for the first time in LHAS crystals. The mechanical strength was confirmed from microhardness study and void volume. Due to the low value of the dielectric constant, and good piezoelectric and ferroelectric properties, LHAS crystals can be used in microelectronics, sensors and advanced electronic devices.



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

2016-08-01

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+.



On the effective ionic radii for ammonium

2016-08-01

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 Å (CN = IV), 1.48 Å (CN = VI), 1.54 Å (CN = VIII) and 1.67 Å (CN = XII). The bond-valence parameters r0 = 2.3433 Å and B = 0.262 Å have been determined for ammonium–fluorine bonds.



Structure and topology of three-dimensional hydrocarbon polymers

2016-08-01

A new family of three-dimensional hydrocarbon polymers which are more energetically favorable than benzene is proposed. Although structurally these polymers are closely related to well known diamond and lonsdaleite carbon structures, using topological arguments we demonstrate that they have no known structural analogs. Topological considerations also give some indication of possible methods of synthesis. Taking into account their exceptional optical, structural and mechanical properties these polymers might have interesting applications.



Modulated crystal structure of InMo4O6

2016-08-01

The (3 + 1)-dimensional modulated crystal structure of the metal-rich cluster compound InMo4O6 was solved and refined from single-crystal data in the superspace group P4/mbm(00γ)00ss [q = 0, 0, 0.1536 (4); a = 9.6664 (9), c = 2.8645 (3) Å; R1(all) = 0.046, wR(all) = 0.076]. The crystal structure is closely related to the NaMo4O6 structure type. It is built from rods of Mo6 clusters condensed via trans edges. These form channels parallel to [001], in which In6 and In7 oligomers alternate. Weak diffuse planes parallel to (001)* interconnect the satellite reflections; they occur due to two-dimensional rod disorder of the In oligomer chains.



Structures of N-acetyl-dl-isoleucine, N-acetyl-dl-alloisoleucine and their ammonium salts; role of ammonium ions in crystal structure formation

2016-08-01

The crystal structures of N-acetyl-dl-isoleucine, N-acetyl-dl-alloisoleucine and their ammonium salts show that these four compounds exist as racemic compounds around room temperature. The two ammonium salts are arranged around a 21 screw axis, forming a helical column which consists of ammonium ions and single enantiomeric anions similar to the crystals of the ammonium salts of optically active N-acetyl-l-isoleucine and N-acetyl-d-alloisoleucine. The ammonium ion and the carboxylate ion in the helix are connected by three hydrogen bonds, the fourth hydrogen bond being formed between the ammonium ion and an external acetyl amino group of the neighboring helical column. The fourth hydrogen bond is formed between the ammonium ion and an external acetyl amino group of the neighboring 21 column. Ammonium N-acetyl-dl-alloisoleucinate was revealed to exist as an unstable racemic compound due to conformational similarity between the racemic and optically active compounds in the solid state and was optically resolved by fractional crystallization at 293 K.