Frontiers of molecular crystal structure prediction for pharmaceuticals and functional organic materials

The reliability of organic molecular crystal structure prediction has improved tremendously in recent years. Crystal structure predictions for small, mostly rigid molecules are quickly becoming routine. Structure predictions for larger, highly flexible molecules are more challenging, but their crystal structures can also now be predicted with increasing rates of success. These advances are ushering in a new era where crystal structure prediction drives the experimental discovery of new solid forms. After briefly discussing the computational methods that enable successful crystal structure prediction, this perspective presents case studies from the literature that demonstrate how state-of-the-art crystal structure prediction can transform how scientists approach problems involving the organic solid state. Applications to pharmaceuticals, porous organic materials, photomechanical crystals, organic semi-conductors, and nuclear magnetic resonance crystallography are included. Finally, efforts to improve our understanding of which predicted crystal structures can actually be produced experimentally and other outstanding challenges are discussed.

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.

Pillararene-Based Variable Stoichiometry Co-Crystallization: A Versatile Approach to Diversified Solid-State Superstructures

Variable stoichiometry co-crystals are important in solid-state supramolecular chemistry as they allow studies of structure-property relationships while permitting the synthesis of new scaffolds using identical synthons. In this work, we extend the concept of variable stoichiometry co-crystals into the realm of pillararene chemistry and show that this permits the rational construction of a diverse set of supramolecular structures in the solid state. Specifically, we report a series of variable stoichiometry co-crystals based on pillar[n]arenes and tetracyanobenzene (TCNB) and show that the combination of in-cavity complexation by pillar[n]arenes (n = 5,6) and outside binding with TCNB allows several types of co-crystals with different self-assembled superstructures to be isolated. The variable stoichiometry co-crystals of this study display different solid-state physicochemical properties, including colors and luminescence features. Among these pillar[n]arene-based co-crystals, we discovered unique crystallographic architectures wherein two sets of individual host-guest complexes co-exist in the solid state. These mixed co-crystal systems allow for vapochromic-based detection of n-bromoalkanes. This work highlights a new strategy for the construction of self-assembled superstructures in the solid state and for tuning their intrinsic characteristics, including their luminescent and substrate-responsive features.

Polymorphism of Purpurin and Low-level Detection of the Noncentrosymmetric form by Second Harmonic Generation Microscopy

Nonlinear optical imaging based on second harmonic generation (SHG) provides rapid and highly selective detection of polar crystals. Purpurin (PUR) is a natural product with multiple pharmacological activities. Two polymorphs of PUR show distinct crystal packing and structural symmetry, where form I crystallizes in a polar space group and form II crystallizes in a centrosymmetric crystal structure. The two polymorphs are monotropically related, with form I being the thermodynamically stable form, as suggested by slurry experiments, in-situ Raman spectroscopy and crystal structure prediction (CSP). The specificity of SHG to the polar crystals of form I allows rapid polymorphism detection at the limit of individual crystals. SHG is also able to detect low levels of form I in a tablet matrix dominated by amorphous excipients. This study shows that SHG microscopy can achieve the rapid and sensitive detection of noncentrosymmetric crystals in solid dosage forms, which is especially helpful for the early detection of unwanted polymorphic conversion or crystallization of amorphous drugs in formulations and final products.

Variable stoichiometry cocrystals: occurrence and significance

Stoichiometric variation in organic cocrystals, their synthesis, structure elucidation and properties are discussed. Accountable reasons for the occurrence of such cocrystals are emphasised.

On the entropy cost of making solvates

We present a simple way of estimating the entropy cost of solvate formation in crystals. The entropy penalty of making solvates can be as low as <1 kJ mol^-1 or as high as >9 kJ mol^-1 and is entirely dependent on the nature of the liquid component and the temperature of solvate formation. A link is found between a low entropy cost and a higher likelihood for a solvent to make solvates.

Experimental and computational approaches to rationalise multicomponent supramolecular assemblies: dapsone monosolvates

The monosolvate crystal energy landscapes of dapsone (DDS) including the solvents carbon tetrachloride, acetone, cyclohexanone, dimethyl formamide, tetrahydrofuran, methyl ethyl ketone, 1,2-dichloroethane, 1,4-dioxane, dichloromethane and chloroform were established using experimental and computational approaches. To rationalise and understand solvate formation, solvate stability and desolvation reactions a careful control of the experimental crystallisation and storage conditions, a range of thermoanalytical methods and crystal structure prediction were required. Six of the eight DDS monosolvates are reported and characterised for the first time. Structural similarity and diversity of the at ambient conditions unstable monosolvates were apparent from the computed crystal energy landscapes, which had the experimental packings as lowest energy structures. The computed structures were used as input for Rietveld refinements and isostructurality of four of the monosolvates was confirmed. Packing comparisons of the solvate structures and molecular properties of the solvent molecules indicated that both size/shape of the solvent molecule and the possible DDSsolvent interactions are the important factors for DDS solvate formation. Through the combination of experiment and theory solvate stability and structural features have been rationalised.

Metal-free mechanochemical oxidations in Ertalyte® jars

Aimed at eliminating or at least significantly reducing the use of solvents, sodium hypochlorite pentahydrate crystals (NaOCl·5H2O) in the presence of a catalytic amount of a nitrosyl radical (TEMPO or AZADO) have been successfully used to induce mechanochemical oxidative processes on several structurally different primary and secondary alcohols. The proposed redox process is safe, inexpensive and performing effectively, especially on the macroscale. Herein, an Ertalyte® jar has been successfully used, for the first time, in a mechanochemical process.

Explaining crystallization preferences of two polyphenolic diastereoisomers by crystal structure prediction

Crystal structure prediction is used to understand the differences in crystallization of catechin and epicatechin, and to explore the predictability of solvate formation.

Synthon hierarchy in theobromine cocrystals with hydroxybenzoic acids as coformers

Cocrystals, solids composed of molecular and/or ionic compounds connected by noncovalent interactions, are objects of interest in crystal engineering. Theobromine, as an active pharmaceutical ingredient, was used in cocrystallization with dihydroxybenzoic acids.

On the kinetics of solvate formation through mechanochemistry

We demonstrate that solvates obtained through mechanochemistry are the thermodynamic products, and that the kinetics of solvate formation are related to the easiness of breaking the reactant crystals.

Energy-Structure-Function Maps: Cartography for Materials Discovery

Some of the most successful approaches to structural design in materials chemistry have exploited strong directional bonds, whose geometric reliability lends predictability to solid-state assembly. For example, metal-organic frameworks are an important design platform in materials chemistry. By contrast, the structure of molecular crystals is defined by a balance of weaker intermolecular forces, and small changes to the molecular building blocks can lead to large changes in crystal packing. Hence, empirical rules are inherently less reliable for engineering the structures of molecular solids. Energy-structure-function (ESF) maps are a new approach for the discovery of functional organic crystals. These maps fuse crystal-structure prediction with the computation of physical properties to allow researchers to choose the most promising molecule for a given application, prior to its synthesis. ESF maps were used recently to discover a highly porous molecular crystal that has a high methane deliverable capacity and the lowest density molecular crystal reported to date (r = 0.41 g cm^-3 , SA_BET = 3425 m² g^-1 ). Progress in this field is reviewed, with emphasis on the future opportunities and challenges for a design strategy based on computed ESF maps.

Evaluating the Energetic Driving Force for Cocrystal Formation

We present a periodic density functional theory study of the stability of 350 organic cocrystals relative to their pure single-component structures, the largest study of cocrystals yet performed with high-level computational methods. Our calculations demonstrate that cocrystals are on average 8 kJ mol^-1 more stable than their constituent single-component structures and are very rarely (<5% of cases) less stable; cocrystallization is almost always a thermodynamically favorable process. We consider the variation in stability between different categories of systems-hydrogen-bonded, halogen-bonded, and weakly bound cocrystals-finding that, contrary to chemical intuition, the presence of hydrogen or halogen bond interactions is not necessarily a good predictor of stability. Finally, we investigate the correlation of the relative stability with simple chemical descriptors: changes in packing efficiency and hydrogen bond strength. We find some broad qualitative agreement with chemical intuition-more densely packed cocrystals with stronger hydrogen bonding tend to be more stable-but the relationship is weak, suggesting that such simple descriptors do not capture the complex balance of interactions driving cocrystallization. Our conclusions suggest that while cocrystallization is often a thermodynamically favorable process, it remains difficult to formulate general rules to guide synthesis, highlighting the continued importance of high-level computation in predicting and rationalizing such systems.

From serendipity to supramolecular design: assessing the utility of computed crystal form landscapes in inferring the risks of crystal hydration in carboxylic acids

Calculated structural descriptors for predicted anhydrate polymorphs are used to assess the risks of crystal hydration in carboxylic acids.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129 Xe NMR Spectroscopy

An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o- and m-fluorophenol, whose previously unknown clathrate structures have been studied by ¹²⁹ Xe NMR spectroscopy. The high sensitivity of the ¹²⁹ Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures.

Why do Hydrates (Solvates) Form in Small Neutral Organic Molecules? Exploring the Crystal Form Landscapes of the Alkaloids Brucine and Strychnine

Computational methods were used to generate and explore the crystal structure landscapes of the two alkaloids strychnine and brucine. The computed structures were analyzed and rationalized by correlating the modelling results to a rich pool of available experimental data. Despite their structural similarity, the two compounds show marked differences in the formation of solid forms. For strychnine only one anhydrous form is reported in the literature and two new solvates from 1,4-dioxane were detected in the course of this work. In contrast, 22 solid forms are so far known to exist for brucine, comprising two anhydrates, four hydrates (HyA - HyC and a 5.25-hydrate), twelve solvates (alcohols and acetone) and four heterosolvates (mixed solvates with water and alcohols). For strychnine it is hard to produce any solid form other than the stable anhydrate while the formation of specific solid state forms of brucine is governed by a complex interplay between temperature and relative humidity/water activity and it is rather a challenging to avoid hydrate formation. Differences in crystal packing and the high tendency for brucine to form hydrates are not intuitive from the molecular structure alone, as both molecules have hydrogen bond acceptor groups but lack hydrogen bond donor groups. Only the evaluation of the crystal energy landscapes, in particular the close-packed crystal structures and high-energy open frameworks containing voids of molecular (water) dimensions, allowed us to unravel the diverse solid state behavior of the two alkaloids at a molecular level. In this study we demonstrate that expanding the analysis of anhydrate crystal energy landscapes to higher energy structures and calculating the solvent-accessible volume can be used to estimate non-stoichiometric or channel hydrate (solvate) formation, without explicitly computing the hydrate/solvate crystal energy landscapes.

Predicting solvent effects on the structure of porous organic molecules

A computational approach for the prediction of the open, metastable, conformations of porous organic molecules in the presence of solvent is developed.

Modeling Polymorphic Molecular Crystals with Electronic Structure Theory

Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.

High pressure used for producing a new solvate of 1,4-diazabicyclo[2.2.2]octane hydroiodide

Above 3.1 GPa, the solvate with water and methanol is formed, which cannot be obtained at normal pressure.

Guest control of structure in porous organic cages

Two porous organic cages with different thermodynamic polymorphs were induced by co-solvents to interchange their crystal packing modes, thus achieving guest-mediated control over solid-state porosity. In situ crystallography allows the effect of the co-solvent guests on these structural interconversions to be understood.

Solid state forms of 4-aminoquinaldine - From void structures with and without solvent inclusion to close packing

Polymorphs of 4-aminoquinaldine (4-AQ) have been predicted in silico and experimentally identified and characterised. The two metastable forms, AH (anhydrate) II and AH III, crystallise in the trigonal space group [Formula: see text] and are less densely packed than the thermodynamically most stable phase AH I° (P21/c ). AH II can crystallise and exist both, as a solvent inclusion compound and as an unsolvated phase. The third polymorph, AH III, is exclusively obtained by desolvation of a carbon tetrachloride solvate. Theoretical calculations correctly estimated the experimental 0K stability order, confirmed that AH II can exist without solvents, gave access to the AH III structure, and identified that there exists a subtle balance between close packing and number of hydrogen bonding interactions in the solid state of anhydrous 4-AQ. Furthermore, the prevalence of void space and solvent inclusion in [Formula: see text] structures is discussed.

Co-crystallisation of cytosine with 1,10-phenanthroline: computational screening and experimental realisation

Crystal structure prediction calculations applied to co-crystals of 1,10-phenanthroline and nucleobases (A, T, C, G) show that only cytosine is expected to form a 1 : 1 co-crystal. Experiments provide verification for this result although the observed co-crystal crystallises with Z′ = 2, not Z′ = 1.

Solvent-guest control of two extremely similar tetrahydrofuran inclusion structures

Racemic 2,4,6,8-tetracarbomethoxybicyclo[3.3.0]octa-2,6-diene-3,7-diol, C16H18O10 (1), was known previously to yield two solvent-free polymorphs and also a clathrate inclusion crystal form. Crystallization of (1) yields two inclusion compounds containing tetrahydrofuran (THF): (1)4·THF is obtained from a mixture of THF and methanol, whereas (1)2·THF is obtained from pure THF. The X-ray crystal structures reveal that the two compounds are extremely similar and that their host arrangements are essentially identical. They differ, however, in the proportion, orientation and host-guest interaction of the included THF molecules. The disordered guest molecules in (1)4·THF are oriented along the guest channel direction, whereas in (1)2·THF they lie across the channel. This unusual solvent-guest control of inclusion structures has implications relating to the formation of polymorphic structures and other competing crystal forms.

Which conformations make stable crystal structures? Mapping crystalline molecular geometries to the conformational energy landscape

Flexible organic molecules often do not adopt their lowest energy conformer in crystal structures. We find that there is a preference for molecules to crystallise with high surface area conformers.

Pharmaceutical hydrates under ambient conditions from high-pressure seeds: a case study of GABA monohydrate

A monohydrate form of the neurotransmitter γ-amino butyric acid (GABA) has been crystallised in the 0.4–0.8 GPa pressure range, recovered to ambient pressure and then used as a seed. Theoretical calculations have been used to rationalise the experimental observations and gain an insight into thermodynamic stability.

De novo determination of the crystal structure of a large drug molecule by crystal structure prediction-based powder NMR crystallography

The crystal structure of form 4 of the drug 4-[4-(2-adamantylcarbamoyl)-5-tert-butyl-pyrazol-1-yl]benzoic acid is determined using a protocol for NMR powder crystallography at natural isotopic abundance combining solid-state (1)H NMR spectroscopy, crystal structure prediction, and density functional theory chemical shift calculations. This is the first example of NMR crystal structure determination for a molecular compound of previously unknown structure, and at 422 g/mol this is the largest compound to which this method has been applied so far.

Why don't we find more polymorphs?

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Polymorph identification and crystal structure determination by a combined crystal structure prediction and transmission electron microscopy approach

Electron diffraction offers advantages over X-ray based methods for crystal structure determination because it can be applied to sub-micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline.

Tris(hydroxymethyl) aminomethane salt of ramipril: synthesis, structural characterization from X-ray powder diffraction and stability studies

Tris(hydroxymethyl) aminomethane (tris) salt of API ramipril was synthesized, and characterized by FTIR, TG-DSC and ab initio X-ray powder structure analysis. The compound, ramipril-tris (II), crystallizes in the monoclinic space group P2(1) with a=24.3341(15), b=6.4645(5), c=9.5357(7) Å, β=96.917(3)° and V=1489.1(3) Å(3). The crystal structure has been determined from laboratory X-ray powder diffraction data using direct space global optimization strategy (simulated annealing) followed by the Rietveld refinement. A network of intermolecular OH…O, CH…N and CH…O hydrogen bonds between the ramipril-ramipril, tris-tris and ramipril-tris components in the compound generates a two-dimensional molecular assembly in (110) plane. A comparative study of solid-state stabilities of ramipril-tris (II) with that of ramipril (I) and ramipril-erbumine (III) indicates that ramipril-tris (II) is the most stable one among the three, and the conversion to impurity D after 72 h at 80 °C is only 1.5%. The solution phase analysis at different pH values also reveals a greater stability of ramipril-tris (II) over ramipril (I).

A perspective on synthetic and solid-form enablement of inhalation candidates

The administration of compounds by a dry-powder inhaler presents significant challenges to the development and discovery chemist, owing to the stringent requirements placed upon the physical characteristics of the active pharmaceutical ingredient and the high complexity of the molecules concerned. The current state of synthetic chemistry technology is such that commercial syntheses of these compounds are demanding but achievable. While synthetic chemistry will remain a major component of the development of inhaled therapies, the main challenge facing practitioners in this area is the early identification of a suitable solid form. Further advances in the prediction of solid-form properties would significantly enable this field and may allow triage of molecules to be carried out at the design stage of projects.

Which, if any, hydrates will crystallise? Predicting hydrate formation of two dihydroxybenzoic acids

A study of two dihydroxybenzoic acid isomers shows that computational methods can be used to predict hydrate formation, the compound:water ratio and hydrate crystal structures. The calculations also help identify a novel hydrate found in the solid form screening that validates this study.

Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction

The range of target structures in the fifth international blind test of crystal structure prediction was extended to include a highly flexible molecule, (benzyl-(4-(4-methyl-5-(p-tolylsulfonyl)-1,3-thiazol-2-yl)phenyl)carbamate, as a challenge representative of modern pharmaceuticals. Two of the groups participating in the blind test independently predicted the correct structure. The methods they used are described and contrasted, and the implications of the capability to tackle molecules of this complexity are discussed.

Benefits of cocrystallisation in pharmaceutical materials science: an update

Objectives

We provide a brief overview of recent applications of cocrystals for improving the physico-chemical and materials properties of active pharmaceutical ingredients, including solubility, humidity and thermal stability, dissolution rates and compressibility for tablet formation.

Key findings

This overview illustrates the pharmaceutical applications of cocrystals, with a selection of recent examples and also attempts to foresee future developments by proposing several directions not yet explored in the area of pharmaceutical cocrystallisation.

Summary

Reliable strategies for the synthesis and design of pharmaceutical cocrystals have now been established, and the potential of cocrystallisation for enhancing the solid-state properties of drugs is well recognised; the field is now moving towards the understanding of cocrystal structure–property relationships, for which systematic structural studies and computational approaches will play a key role.