Predicting crystal form stability under real-world conditions.

The physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2-4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid-solid free-energy differences, quantifying statistical errors for the computed free energies and placing both hydrate crystal structures of different stoichiometries and anhydrate crystal structures on the same energy landscape, with defined error bars, as a function of temperature and relative humidity. The calculated free energies have standard errors of 1-2 kJ mol-1 for industrially relevant compounds, and the method to place crystal structures with different hydrate stoichiometries on the same energy landscape can be extended to other multi-component systems, including solvates. These contributions reduce the gap between the needs of the experimentalist and the capabilities of modern computational tools, transforming crystal structure prediction into a more reliable and actionable procedure that can be used in combination with experimental evidence to direct crystal form selection and establish control5.

Atomic-level structure determination of amorphous molecular solids by NMR.

Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.

A toolbox for improving the workflow of NMR crystallography.

NMR crystallography is a powerful tool with applications in structural characterization and crystal structure verification, to name two. However, applying this tool presents several challenges, especially for industrial users, in terms of consistency, workflow, time consumption, and the requirement for a high level of understanding of experimental solid-state NMR and GIPAW-DFT calculations. Here, we have developed a series of fully parameterized scripts for use in Materials Studio and TopSpin, based on the .magres file format, with a focus on organic molecules (e.g. pharmaceuticals), improving efficiency, robustness, and workflow. We separate these tools into three major categories: performing the DFT calculations, extracting & visualizing the results, and crystallographic modelling. These scripts will rapidly submit fully parameterized CASTEP jobs, extract data from the calculations, assist in visualizing the results, and expedite the process of structural modelling. Accompanied with these tools is a description on their functionality, documentation on how to get started and use the scripts, and links to video tutorials for guiding new users. Through the use of these tools, we hope to facilitate NMR crystallography and to harmonize the process across users.

Structure determination of an amorphous drug through large-scale NMR predictions.

Knowledge of the structure of amorphous solids can direct, for example, the optimization of pharmaceutical formulations, but atomic-level structure determination in amorphous molecular solids has so far not been possible. Solid-state nuclear magnetic resonance (NMR) is among the most popular methods to characterize amorphous materials, and molecular dynamics (MD) simulations can help describe the structure of disordered materials. However, directly relating MD to NMR experiments in molecular solids has been out of reach until now because of the large size of these simulations. Here, using a machine learning model of chemical shifts, we determine the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR experiments with predicted chemical shifts for MD simulations of large systems. From these amorphous structures we then identify H-bonding motifs and relate them to local intermolecular complex formation energies.

Characterization and demonstration of drug compound ring-chain tautomer formation and its impacts on quality control.

Unknown chromatographic peaks, potential impurities, were observed in a series of related compounds. This led to the identification and characterization of tautomeric equilibria. Structural elucidation was required to understand the potential impurity profile, thus impacting method development for quality control. In this work, characterization of the chemical structures, AZ13581258 and AZD5718, and equilibria of the tautomeric forms was performed using a range of advanced analytical techniques such as preparative chromatography, nuclear magnetic resonance (NMR), chromatographic detection by mass spectrometry (MS), MSMS, and ultraviolet spectroscopy (UV). Predictions using density functional theory (DFT) further explains and confirms the tautomer equilibria through predictions of reaction barrier energies, UV-spectra and NMR data. These investigations led to fully understand the impurity profile and to the development of a quality control method for AZD5718 drug substance and drug product. In conclusion, ring-chain tautomeric structures are predominately formed under acidic conditions, and the additional peaks observed in LC during organic impurity determination were found to originate from ring-chain closed tautomers in equilibria with the parent open form compound. Hence, the closed and open tautomer forms should all be considered as the same compound.

A curious case of dynamic disorder in pyrrolidine rings elucidated by NMR crystallography.

A pharmaceutical exhibits differing dynamics in crystallographically distinct pyrrolidine rings despite being nearly related by symmetry, with one performing ring inversions while the other is constrained to torsional librations. Using 13C solid-state magic-angle spinning (MAS) NMR and DFT calculations, we show that this contrast originates from C-HH-C close contacts and less efficient C-Hπ intermolecular interactions observed in the transition state of the constrained pyrrolidine ring, highlighting the influence of the crystallographic environment on the molecular motion.

The crystal structure, morphology and mechanical properties of diaquabis(omeprazolate)magnesium dihydrate.

The crystal structure of diaquabis(omeprazolate)magnesium dihydrate (DABOMD) in the solid state has been determined using single-crystal X-ray diffraction. Single crystals of DABOMD were obtained by slow crystallization in ethanol with water used as an antisolvent. The crystal structure shows a dihydrated salt comprising a magnesium cation coordinating two omeprazolate anions and two water molecules (W1) that are strongly bound to magnesium. In addition, two further water molecules (W2) are more weakly hydrogen-bonded to the pyridine nitrogen atom of each omeprazolate anion. The crystal structure was utilized to estimate key material properties for DABOMD, including crystal habit and mechanical properties, which are required for improved understanding and prediction of the behaviour of particles during pharmaceutical processing such as milling. The results from the material properties calculations indicate that DABOMD exhibits a hexagonal morphology and consists of a flat slip plane through the (100) face. It can be classed as a soft material based on elastic constant calculation and exhibits a two-dimensional hydrogen-bonding framework. Based on the crystal structure, habit and mechanical properties, it is anticipated that DABOMD will experience large disorder accompanied by plastic deformation during milling.

Diels-Alder Reactions with Ethylene and Superelectrophiles.

Diels-Alder reactions have been accomplished with ethylene as the dienophile through the use of inverse-electron demand Diels-Alder chemistry. As a key aspect of the chemistry, the dienes are part of tri- or dicationic superelectrophilic systems. Theoretical calculations reveal that the highly charged superelectrophiles possess exceptionally low lying LUMOs, and this facilitates the cycloaddition chemistry with ethylene. The chemistry has been used to prepare a series of tetrahydroquinoline products. This represents the first application of superelectrophilic activation in a cycloaddition reaction, and a new method of utilizing ethylene as a C2 building block.

Elucidating an Amorphous Form Stabilization Mechanism for Tenapanor Hydrochloride: Crystal Structure Analysis Using X-ray Diffraction, NMR Crystallography, and Molecular Modeling.

By the combined use of powder and single-crystal X-ray diffraction, solid-state NMR, and molecular modeling, the crystal structures of two systems containing the unusually large tenapanor drug molecule have been determined: the free form, ANHY, and a dihydrochloride salt form, 2HCl. Dynamic nuclear polarization (DNP) assisted solid-state NMR (SSNMR) crystallography investigations were found essential for the final assignment and were used to validate the crystal structure of ANHY. From a structural informatics analysis of ANHY and 2HCl, conformational ring differences in one part of the molecule were observed which influence the relative orientation of a methyl group on a ring nitrogen and thereby impact the crystallizability of the dihydrochloride salt. From quantum chemistry calculations, the dynamics between different ring conformations in tenapanor is predicted to be fast. Addition of HCl to tenapanor results in general in a mixture of protonated ring conformers and hence a statistical mix of diastereoisomers which builds up the amorphous form, a-2HCl. This was qualitatively verified by 13C CP/MAS NMR investigations of the amorphous form. Thus, to form any significant amount of the crystalline material 2HCl, which originates from the minor (i.e., energetically less stable) ring conformations, one needs to involve nitrogen deprotonation to allow exchange between the minor and major conformations of ANHY in solution. Thus, by controlling the solution pH value to well below the p Ka of ANHY, the equilibrium between ANHY and 2HCl can be controlled and by this mechanism the crystallization of 2HCl can be avoided and the amorphous form of the dichloride salt can therefore be stabilized.

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease.

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (1H, 13C, 15N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13C shift tensors and the observation of residual dipolar coupling between 13C and 14N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Tetra- and Pentacationic Electrophiles and Their Chemistry.

A tetracationic electrophile has been generated in superacid and shown to undergo an arylation reaction with benzene. A cyclization product is also obtained in the absence of benzene, presumably from a tricationic intermediate. Using low-temperature NMR, the tetracationic species is directly observed from a FSO3H-SbF5-SO2ClF solution. Similar chemistry is described with a system involving penta- and tetracationic intermediates. These highly ionized structures and their chemistry were also examined by DFT calculation.

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

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.

Organotrifluoroborates as attractive self-assembling systems: the case of bifunctional dipotassium phenylene-1,4-bis(trifluoroborate).

The first structure of an aromatic bis(trifluoroborate) dipotassium salt, elucidated by the combination of crystallography, DFT calculations, topological and non-covalent interaction analysis, discloses a 3D network undergoing spontaneous self-assembly thanks to the massive participation of weak intra- and intermolecular interactions for which fluorine atoms proved to play a leading role.

Role of the base in Buchwald-Hartwig amination.

The Buchwald-Hartwig amination has been investigated theoretically and experimentally to examine the scope of possible bases under different reaction conditions. Nonpolar solvents resist the formation of new charges. Therefore, the base should be anionic to be able to deprotonate the neutral palladium-amine complex and/or expel the anionic leaving group (bromide). The calculated barrier for the organic base DBU was found to be prohibitively high. In polar solvent, dissociation of bromide becomes possible, but here the base will instead form a complex with palladium, creating an overly stable resting state. The conclusions for both solvent classes hold for both a hindered monodentate phosphine and the labile bidentate ligand BINAP. The computational studies were supported by experimental testing of a range of bases using BINAP in two different solvents, toluene and DMF.

Dicationic ring-opening reactions of trans-2-phenylcyclopropylamine·HCl: electrophilic cleavage of the distal (C2-C3) bond of cyclopropanes.

Electrophilic ring opening of trans-2-phenylcyclopropylamine·HCl occurs at the distal (C2-C3) bond. This is consistent with weakening of the distal bond by the σ-withdrawing ammonium group and charge-charge repulsive effects in the transition state.

Friedel-Crafts-type reactions with ureas and thioureas.

Despite the relatively low reactivities of urea and thiourea functional groups towards nucleophilic attack, we have found conditions in which they are useful substrates in Friedel-Crafts reactions. The Brønsted superacid, triflic acid, promotes these reactions and a mechanism is proposed involving dicationic, superelectrophilic intermediates.