Crystal Structure Prediction Study Research Articles

Two polymorphs of a new AIEgen from transition-metal-free cross-coupling reactions: A combined experimental and crystal structure prediction study

We synthesized a new double aromatic pyrrole [2,5-bis(2,5-dimethoxyphenyl)-1H-pyrrole, abbreviated as BDMP] without using transition metals. This compound exhibits a conjugated skeleton, ideal for aggregation-induced emission luminogens (AIEgens). Two methods, Lewis acid catalysis and photoreaction, were used for synthesis. Different methods produce different crystal structures with the same molecular skeleton. The crystals show different AIE properties. The photocatalytically formed crystal (BDMP-B) is highly luminescent with a 10.4 % fluorescence yield. In contrast, the Lewis acid-catalyzed crystal (BDMP-A) has a lower fluorescence yield of 3.0 %. These differences in emission are due to varying crystal packings, confirmed by quantum calculations.To understand these differences, Crystal Structure Prediction (CSP) studies were conducted. Our goal was to find if more stable crystal packings exist. Several energy ranking approaches were used to identify the most feasible polymorphic forms. These approaches include static lattice energy, lattice binding energy, enthalpy, cohesive enthalpy, Gibbs Free Energy, cohesive Gibbs Free Energy, and high-accurate electronic binding energy from large molecule-cluster crystal packings. Our findings suggest that the most stable crystal forms can be predicted accurately using appropriate theoretical methods.This research improves our understanding of AIEgens. It shows the value of combining experimental work with both cost-effective and highly accurate theoretical methods for crystal structure analysis and prediction.

Packing Preferences of Chalcones: A Model Conjugated Pharmaceutical Scaffold.

We sought the crystal packing preferences of the chalcone scaffold by analyzing 232 single-component crystal structures of chalcones with a small (six or fewer non-hydrogen atoms) substituent on either or both rings, including the unsubstituted molecule. This covers 216 molecules, as some are polymorphic, and 277 independent molecular conformations, as 16% of the crystal structures have more than one symmetry independent molecule. Quantum mechanical conformational profiles of the unsubstituted molecule and the almost 5000 crystal structures within 20 kJ mol–1 of the global minimum generated in a crystal structure prediction (CSP) study have been used to complement this analysis. Although π conjugation would be expected to favor a planar molecule, there are a significant number of crystal structures containing nonplanar molecules with an approximately 50° angle between the aromatic rings. The relative orientations of the molecules in the inversion-related dimers and translation-related dimers in the experimental crystal structures show the same trends as in the CSP-generated structures for the unsubstituted molecule, allowing for the substituent making the side-to-side distances larger. There is no type of dimer geometry associated with particularly favorable lattice energies for the chalcone core. Less than a third of the experimental structures show a face-to-face contact associated with π···π stacking. Analysis of the experimental crystal structures with XPac and Mercury finds various pairs of isostructural crystals, but the largest isostructural set had only 15 structures, with all substituents (mainly halogens) in the para position. The most common one-dimensional motif, found in half of the experimental crystal structures, is a translation-related side-to-side packing, which can be adopted by all the observed conformations. This close-packed motif can be adopted by chalcones with a particularly wide variety of substituents as the substituents are at the periphery. Thus, although the crystal structures of the substituted chalcones show thermodynamically plausible packings of the chalcone scaffold, there is little evidence for any crystal engineering principle of preferred chalcone scaffold packing beyond close packing of the specific molecule.

Combining Structural Rugosity and Crystal Packing Comparison: A Route to More Polymorphs?

In this study, we have combined structural comparisons and the rugosity model to investigate experimental and predicted crystal structures from previous results of a crystal structure prediction study on a group of three rigid, planar small molecules, 2-methyl-, 3-methyl-, and 2,3-dimethyl-benzo[b]thiophene 1,1-dioxide. The results of the crystal structure comparisons provided some insights into the possibility that pairs of predictions, close in energy, might be related by potential phase transitions. In particular, we observed that for some pairs of predictions, a transformation from one type of crystal packing to the other would require only small shifts between adjacent molecules. This raised the question of whether only a few of these predictions can effectively be experimentally isolated. The calculations of the structural rugosity, a parameter that correlates surface rugosity with ease of crystallization, indicated smooth surfaces only for a few predictions. With the aim to isolate new polymorphs, we performed a small experimental study, limited to a few common solvents and crystallizations from the melt. Crystallizations from the melt selectively produced single crystals of new polymorphs for the 3-methyl- and the 2,3-methyl-benzothiophene derivatives. These showed good correlations with the above calculations, suggesting that the combination of crystal structure analysis and experimental screening might represent a useful approach in polymorphism screenings.

Synthesis, crystal structure, and ADME prediction studies of novel imidazopyrimidines as antibacterial and cytotoxic agents.

In the present study, a novel series of polyfunctionalized imidazopyrimidines 6a-u and 9a-d were efficiently constructed by a domino reaction between 2-imino-6-substituted-2,3-dihydropyrimidin-4(1H)-ones 4a-d or 8a-c and 2-bromoacetophenones 5a-i under mild basic conditions. The synthesized series were screened for their antibacterial activity against Staphylococcus aureus and Bacillus subtilis as Gram-positive (+) bacteria, as well as against Gram-negative (-) bacteria Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Salmonella typhi. Most of the synthesized derivatives of imidazopyrimidines 6 and 9 showed remarkable selectivity against Gram(-) bacteria over the Gram(+) ones. Compounds 6c, 6f, and 6g displayed potent and broad-spectrum antibacterial activity against all tested strains. Compounds 6f and 6g displayed promising inhibitory activity on GryB ATPase from E. coli with IC50 = 1.14 and 0.73 μM, respectively. Simultaneously, some of the synthesized imidazopyrimidines were screened for their antiproliferative activity against 60 cancer cell lines at a concentration of 10 μM. Compound 9d showed potent activity against most of the tested cell lines, with a mean growth inhibition of 37%. The ADME (absorption, distribution, metabolism, and excretion) prediction study demonstrated that the synthesized hits have, in addition to their promising chemotherapeutic activity, acceptable pharmacokinetic properties, and a drug-likeness nature to be further developed.

First-Principles Crystal Structure Prediction of Cu(I)-TCNQ Polymorphs

There is a lack of consensus on the crystal structure and polymorphism of Cu(I)-TCNQ, even though an enormous work and great achievements have been reported along decades. This motivated us to perform a crystal structure prediction study (by using FFCASP) combined with total energy calculations at DFT-D level. The ensemble of the optimized structures falls in two distinct regions based on the energy-density phase space. Our predictions located the thermodynamic phase (as a global minimum) and a conformationally similar local minimum structure to the experimentally proposed phase I, in the low- and high-density regions respectively. The Rietveld refinement of P2 1 2 1 2 local minimum structure to the experimental XRD pattern resulted in a structure with a density between the two regions. This polymorph, the kinetic product, becomes a high energy local minimum structure after the full geometry optimization, being 35.03 kJ/mol above the global minimum. In addition, we found that the transition from the high-...

Exploring the Multi-minima Behavior of Small Molecule Crystal Polymorphs at Finite Temperature

The predicted ambient-temperature crystal structures of organic small molecules are often represented by a single energy-minimized configuration at 0 K. This procedure effectively collapses the ensemble of configurations that would be present at ambient temperature into a single representative structure. This simplification is likely to break down if the crystal structure has multiple different lattice-energy minima within the ambient-temperature ensemble. In this work, we explore the existence of multiple minima within finite-temperature crystal basins by sampling crystals at a range of temperatures followed by rapidly quenching the configurations. We then observe whether each crystal returns to the original minimum or to an ensemble of minima on the lattice-energy landscape. Eight of the twelve compounds examined in this work have at least one polymorph with multi-minima behavior. These multi-minima basins have implications for crystal structure prediction studies, and it is therefore important to under...

Dissecting the Conformational and Interaction Topological Landscape of N-ethynylphenylbenzamide by the Device of Polymorphic Diversity

The modern day crystal engineering approach aims at the exploration of the structural landscape of a molecule to perceive the phenomenon of the crystallization event for that molecule. The present study focuses on thorough experimental and computational investigations of the crystal landscape in the conformationally flexible N-ethynylphenylbenzamide molecule. We have performed the chemical modification of the parent unsubstituted N-ethynylphenylbenzamide molecule on the benzoyl ring by different halogen substitutions (monofluoro/difluoro/trifluoromethyl/chloro/bromo) at ortho/meta/para positions and employed the device of the polymorphophore concept to access a large number of experimentally viable structures in the landscape. In a total of 11 substituents as variants in molecules, the parent molecule displays monomorphic behavior, and in the remaining 10 molecules, each exists in several polymorphic forms resulting in a total of 28 single-component crystal structures. Through the systematic analysis of their conformational preferences in the conformational landscape and classification of the prevalent supramolecular recognition patterns, the interaction topologies of all substituent modified polymorphic structures have been mapped by the quantification of interaction energies of supramolecular synthons followed by a crystal structure prediction study. The combination of all studies demonstrates the robustness of primary synthon topology (formed by N–H···O═C/ π···π stacking interaction) and local variation of structures by different secondary interaction preferences (weak C–H···O, C–H···π, C–H···F/Cl/Br, and π···π interactions) to construct a nearly similar global interaction topology of molecules in all crystal structures and represents a general interaction topological landscape.

Topochemical Path in High Lithiation of MoS2

Lithiation of MoS2/RGO (reduced graphite oxide) electrodes repeatedly reached experimental capacities larger than 1000 mA·g–1, corresponding to at least 6 lithium equivalents per gram of MoS2. At our best knowledge, a convincing explanation is still missing in literature. In most cases, phase separation into Li2S and elemental Mo was assumed to occur. However, this can only explain capacities up to 669 mA·g–1, corresponding to an exchange of four Li. Formation of LiMo alloys could resolve the problem but the Li/Mo system does not contain any binary phases. If signs for Li2S formation were found, indeed experimental capacities were below 700 mAh·g–1. Here we present a topochemical mechanism, which sustains multiple charge/discharge cycles at 1000 mAh·g–1, corresponding to an exchange of at least 6 Li per formula unit MoS2. This topochemical reaction route prevents decomposition into binary phases and thus avoids segregation of the components of MoS2. Throughout the whole lithiation/delithiation process, distinct layers of Mo are preserved but extended or shrunk by slight movements and reshuffling of sulfur and lithium atoms. On addition of 6 Li per formula unit to MoS2, all central sulfur atoms are hosted in mutual Mo–S layers such that formal S2– and Mo2– anions appear coordinated by lithium cations. Indeed, similar structures are known in the field of Zintl phases. Our first‐principles crystal structure prediction study describes this topological path through conversion reactions during the lithiation/delithiation processes. All optimized phases along the topological path exhibit a distinct Mo layering giving rise to a series of dominant scattering into pseudo 001 reflections perpendicular to these Mo planes. The mechanism we present here explains why such high capacities can be reached reversibly for MoS2/RGO nano composites

The importance of configurational disorder in crystal structure prediction: the case of loratadine.

Loratadine, an over-the-counter antihistamine medication, has two known monotropically related polymorphs, both of which feature disorder. A combined experimental and computational approach using variable temperature single crystal X-ray diffraction (VT-SCXRD) analysis and dispersion corrected density functional theory (DFT-D) reveals that the nature of the disorder in each form is markedly different and cannot be described by a simple isolated-site model with thermally populated conformations in either of the two cases. In Form I, the ethyl carbamate functionality adopts two different configurations, with adjacent moieties interacting along one-dimensional chains. The most stable arrangement features alternating configurations, but because of the low energetic cost of stacking faults, the domain sizes are short and an average crystal structure is observed experimentally. The configurational free energy of the disordered structure is lower than the energy of the two corresponding ordered crystal structures, but the energy decrease is dominated by the lower lattice energy of the alternating arrangement with a small entropic contribution. In Form II, the flexible cycloheptane bridge adopts two different configurations. The disorder is not an equilibrium property but is instead frozen-in during the crystallisation process. The configurational free energy of the disordered structure falls in between the lattice energies of the two corresponding ordered structures. The two ordered components of each disordered structure are all found in a crystal structure prediction (CSP) study with the GRACE programme. However, the experimentally observed stability relationship is only reproduced when the energy contribution of disorder is taken into account. The disordered model of Form I is found to be lower in energy than all the other predicted structures and there is no indication of a missing, thermodynamically more stable, form. The case of loratadine demonstrates that experimentally observed disorder close to 50/50 does not necessarily correspond to a free energy decrease by kT ln 2.

How many ritonavir cases are there still out there?

Based on a thorough and critical analysis of the commercial crystal structure prediction studies of 41 pharmaceutical compounds, we conclude that for between 15 and 45% of all small-molecule drugs currently on the market the most stable experimentally observed polymorph is not the thermodynamically most stable crystal structure and that the appearance of the latter is kinetically hindered.

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

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.

From dimers to the solid-state: Distributed intermolecular force-fields for pyridine.

An anisotropic atom-atom force-field for pyridine, using distributed atomic multipoles, polarizabilities, and dispersion coefficients and an anisotropic atom-atom repulsion model derived from symmetry-adapted perturbation theory (density functional theory) dimer calculations, is used to model pyridine crystal structures. Here we show that this distributed intermolecular force-field (DIFF) models the experimental crystal structures as accurately as modelling all but the electrostatic term with an isotropic repulsion-dispersion potential that has been fitted to experimental crystal structures. In both cases, the differences are comparable to the changes in the crystal structure with temperature, pressure, or neglect of zero-point vibrational effects. A crystal structure prediction study has been carried out, and the observed polymorphs contrasted with hypothetical thermodynamically competitive crystal structures. The DIFF model was able to identify the structure of an unreported high pressure phase of pyridine, unlike the empirically fitted potential. The DIFF model approach therefore provides a model of the underlying pair potential energy surface that we have transferred to the crystalline phase with a considerable degree of success, though the treatment of the many-body terms needs improvement and the pair potential is slightly over-binding. Furthermore, this study of a system that exhibits isotopic polymorphism highlights that the use of an empirical potential has partially absorbed temperature and zero-point motion effects as well as the intermolecular forces not explicitly represented in the functional form. This study therefore highlights the complexity in modelling crystallization phenomena from a realistic pair potential energy surface.

Stable Crystalline Forms of Na Polysulfides: Experiment versus Ab Initio Computational Prediction

For the design of light-metal-sulfur batteries and for the understanding of their performance, knowledge on the stable crystalline polysulfides is very important. We confronted experimental and ab initio crystal structure prediction studies on the stability of Na polysulfides. The selected evolutionary-based structure-prediction algorithm was able to quickly and correctly predict the thermodynamically stable crystalline forms of Na polysulfides with small unit cells. For Na polysulfides with large unit cells, the algorithm correctly proposed short unbranched polysulfide chains to be energetically favorite structural motifs, but could not find proper three-dimensional structures in the limited number of generations. Experimentally, the polysulfides were studied by X-ray diffraction and 23 Na solid-state NMR spectroscopy. Complemented by calculations of the isotropic chemical shifts and quadrupolar coupling constants, NMR spectroscopy proved to be an excellent tool for the examination of Na polysulfides, because it allowed easy distinction and quantification of components in the samples.

4-Aminoquinaldine monohydrate polymorphism: Prediction and impurity aided discovery of a difficult to access stable form.

Crystal structure prediction studies indicated the existence of an unknown high density monohydrate structure (Hy1B°) as global energy minimum for 4-aminoquinaldine (4-AQ). We thus performed an interdisciplinary experimental and computational study elucidating the crystal structures, solid form inter-relationships, kinetic and thermodynamic stabilities of the stable anhydrate (AH I°), the kinetic monohydrate (Hy1A ) and this novel monohydrate polymorph (Hy1B°) of 4-AQ. The crystal structure of Hy1B° was determined by combining laboratory powder X-ray diffraction data and ab initio calculations. Dehydration studies with differential scanning calorimetry and solubility measurements confirmed the result of the lattice energy calculations, which identified Hy1B° as the thermodynamically most stable hydrate form. At 25 °C the equilibrium of the 4-AQ hydrate/anhydrate system was observed at an aw (water activity) of 0.14. The finding of Hy1B° was complicated by the fact that the metastable but kinetically stable Hy1A shows a higher nucleation and growth rate. The presence of an impurity in an available 4-AQ sample facilitated the nucleation of Hy1B°, whose crystallisation is favored under hydrothermal conditions. The value of combining experimental with theoretical studies in hydrate screening and characterisation, as well as the reasons for hydrate formation in 4-AQ, are discussed.

Experimental and computational crystal structure landscape study of nigerloxin: a fungal metabolite from Aspergillus niger

The crystal structure landscape for the bioactive fungal metabolite, nigerloxin, has been explored in the present study using a combined experimental and computational approach. Two new solvate forms of nigerloxin, have been identified from crystallization screening experiments. Additionally, a crystal structure prediction (CSP) study of nigerloxin anhydrate and monohydrate forms has been performed in the study. A comparison of the radical scavenging properties of nigerloxin and related β-hydroxy-γ-pyrone analogues have been performed with the help of bond dissociation enthalpy (BDE) and HOMO–LUMO energy gap computations, which indicate the lowest BDE and HOMO–LUMO gaps for nigerloxin. Various growth units present in the experimental and predicted crystal structures were identified using the supramolecular synthon approach and were utilized in the identification of the most probable crystal growth pathways available for nigerloxin. A total of twelve distinct crystal growth pathways were identified for nigerloxin anhydrate from the CSP based crystal structural landscape study. The 1-D nigerloxin water tape synthon (1HA) was identified as the most frequently observed growth unit in the predicted structures and was also found present in the two experimental solvate forms. The higher order supramolecular constructs derived from the synthon 1HA were identified as the most probable crystal growth pathways for the nigerloxin monohydrate.

Solvent and additive interactions as determinants in the nucleation pathway: general discussion.

Sarah Price opened a general discussion of the paper by Sven Schroeder: I have been generating the thermodynamically plausible crystal structures of organic molecules for many years, and back in 2004 we did a crystal structure prediction (CSP) study on imidazole1 and found that it was relatively straightforward. Following your paper, we have reclassified the low energy structures according to the tilt within the hydrogen-bonded chain and the relative direction of the chains. Although the observed structure was the global minimum, two other structures with a displacement of otherwise identical layers are very close in energy. Do you think that if imidazole had crystallised in one of these alternative structures it would be distinguishable by NEXAFS? This would be a very sensitive test of whether NEXAFS combined with CSP could be used in characterising crystal structures.

Prediction of possible CaMnO3modifications using anab initiominimization data-mining approach

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

Polymorphic Behaviour of 3-Chloromandelic acid

For several years we have been making detailed comparisons of the crystal structures of large sets of related compounds in an attempt to understand the factors determining the adoption of particular molecular arrangements within crystal structures. In all these projects, the XPac program [1] was used to identify similarity between structures in 0-dimensions (0D) (discrete molecular arrangements e.g. dimers, trimers etc),1D (chains or stacks), 2D (sheets or planes) and 3D (frameworks or full isostructurality) as a preliminary to the detailed comparison of the similarities so identified. As part of a larger crystallographic project to investigate the relationship between structure and chirality, we have synthesized and determined crystal structures of families of monosubstituted racemic mandelic acids with fluoro, chloro, bromo, iodo, trifluoromethyl, methyl and methoxy substituents at the ortho, meta and para positions. The substituted mandelic acids are polymorphically prolific and with the inclusion of unsubstituted mandelic acid, 28 structures have been compared. Of special interest has been 3-chloromandelic acid (3-ClMA), for which so far five polymorphs have been discovered: three racemic, two of which are isostructural [2], and two enantiopure. A crystal structure prediction (CSP) study of 3-ClMA has been carried out using the CrystalPredictor [3] and CrystalOptimizer [3] algorithms to generate the crystal energy landscape which is exceptionally dense with 3050 structures within 20 kJ mol-1. Many of these are more stable than the known forms, which is consistent with the complex crystallisation behaviour observed. From our observations of the crystallisation behaviour of substituted chloromandelic acids in general and the CSP study of 3-ClMA, we expect to discover further polymorphs of 3-ClMA and to this end cross-seeding experiments using crystals from differently substituted mandelic acids and a comprehensive polymorph screen are at present being undertaken.

Structure prediction of N-heteroacenes as potential organic semiconductors

Organic electronics offer exciting new alternatives to traditional inorganic devices based on advantages such as lower cost, ease of manufacture and flexibility. Small molecule semiconductors such as pentacene and rubrene are the focus of intense research due to performance approaching that of inorganic semiconductors. Charge transfer in polyaromatic hydrocarbons (PAHs) relies on the degree of π-conjugation and overlap of the π-systems of neighbouring molecules in the solid state. Small changes in the intermolecular interactions can lead to important changes in crystal packing and electronic properties. Thus, functionalization of PAHs is often used to improve their packing in the solid state. The addition of electronegative atoms into the ring system of pentacene has been proposed for improving stability while retaining attractive properties. [1] N-heteroacenes result from the substitution of nitrogen into the arene ring structure. The resulting potential for weak hydrogen bonding could direct coplanar molecular arrangements, sheet formation and favourable π-overlap for charge transport. Theoretical studies [2] have been carried out showing promising properties at the molecular level. As of yet no analysis of the solid state of these molecules has been performed to investigate how this substitution affects the packing and electronic properties. Here, we present the results of crystal structure prediction studies and calculation of charge transport properties aimed at understanding the influence of nitrogen substitution on the crystal packing of N-heteropentacenes and their performance as semiconducting materials.

A molecular picture of the problems in ensuring structural purity of tazofelone

Almost twenty years after the crystal polymorphism of tazofelone was first studied at Lilly, the compound was revisited by calculating the crystal energy landscape and complementing the calculations with experimental work for calibration purposes. The crystal structure prediction study confirmed the stability of racemic form II (RCII) and showed that the racemic compound had greater potential for polymorphism than the single enantiomer. The seeding experiment that has previously been shown to produce a racemic solid solution (SS) correlates with the isostructurality between some low energy racemic structures and the enantiopure form. Other low energy structures have the same layer structure as both racemic polymorphs and the newly-discovered, but closely related, polymorph RCIII, which accounts for the difficulty in obtaining phase pure samples of the metastable RCI and RCIII and the problems of structural purity evidenced by streaked diffraction spots for RCI–III in the single crystal diffraction. This molecular picture of the problems in ensuring structural purity in the layer structure polymorphs of tazofelone not only explains the crystal dependent thermochemistry measurements of tazofelone, but also shows the value of combining a range of experimental and computational techniques to investigate the organic solid state.