Narrowing down the conformational space with solid-state NMR in crystal structure prediction of linezolid cocrystals

Many solids crystallize as microcrystalline powders, thus precluding the application of single crystal X-Ray diffraction in structural elucidation. In such cases, a joint use of high-resolution solid-state NMR and crystal structure prediction (CSP) calculations can be successful. However, for molecules showing significant conformational freedom, the CSP-NMR protocol can meet serious obstacles, including ambiguities in NMR signal assignment and too wide conformational search space to be covered by computational methods in reasonable time. Here, we demonstrate a possible way of avoiding these obstacles and making as much use of the two methods as possible in difficult circumstances. In a simple case, our experiments led to crystal structure elucidation of a cocrystal of linezolid (LIN), a wide-range antibiotic, with 2,3-dihydroxybenzoic acid, while a significantly more challenging case of a cocrystal of LIN with 2,4-dihydroxybenzoic acid led to the identification of the most probable conformations of LIN inside the crystal. Having four rotatable bonds, some of which can assume many discreet values, LIN molecule poses a challenge in establishing its conformation in a solid phase. In our work, a set of 27 conformations were used in CSP calculations to yield model crystal structures to be examined against experimental solid-state NMR data, leading to a reliable identification of the most probable molecular arrangements.

Energetics of carboxylic acid–pyridine heterosynthon revisited: A computational study of intermolecular hydrogen bond domination on phenylacetic acid–nicotinamide cocrystals

Carboxylic acid–pyridine heterosynthon (CPHS) is one of the most common synthons found in cocrystal packing. Phenylacetic acid (PYC)–nicotinamide (NIC) (PYCNIC) cocrystals were used as a computational model to assess the most important factor in the emergence of the synthon. Geometry optimization was carried out on every possible two molecules of PYC–NIC conformation based on B3LYP-D3BJ/6-311G (d,p). Various energetic parameters, including total energy, interaction energy, and hydrogen bond energy, were used to compare the existing conformation to the putative conformation. The conformation with CPHS has −53.87 kJ mol−1 of single intermolecular hydrogen bond energy (EHB), which is the strongest of all. It turns out that there is no other parameter better than EHB to describe the superiority of CPHS in PYCNIC.

Efficient Screening of Coformers for Active Pharmaceutical Ingredient Cocrystallization

Controlling the physical properties of solid forms for active pharmaceutical ingredients (APIs) through cocrystallization is an important part of drug product development. However, it is difficult to know a priori which coformers will form cocrystals with a given API, and the current state-of-the-art for cocrystal discovery involves an expensive, time-consuming, and, at the early stages of pharmaceutical development, API material-limited experimental screen. We propose a systematic, high-throughput computational approach primarily aimed at identifying API/coformer pairs that are unlikely to lead to experimentally observable cocrystals and can therefore be eliminated with only a brief experimental check, from any experimental investigation. On the basis of a well-established crystal structure prediction (CSP) methodology, the proposed approach derives its efficiency by not requiring any expensive quantum mechanical calculations beyond those already performed for the CSP investigation of the neat API itself. The approach and assumptions are tested through a computational investigation on 30 potential 1:1 multicomponent systems (cocrystals and solvate) involving 3 active pharmaceutical ingredients and 9 coformers and one solvent. This is complemented with a detailed experimental investigation of all 30 pairs, which led to the discovery of five new cocrystals (three API-coformer combinations, a polymorphic cocrystal example, and one with different stoichiometries) and a cis-aconitic acid polymorph. The computational approach indicates that, for some APIs, a significant proportion of all potential API/coformer pairs could be investigated with only a brief experimental check, thereby saving considerable experimental effort.

Along the road to Crystal Structure Prediction (CSP) of pharmaceutical-like molecules

Computational methods used for predicting crystal structures of organic compounds are mature enough to be routinely used with many rigid and semi-rigid organic molecules. The usefulness of Crystal Structure Prediction...

Expanding the Solid Form Landscape of Bipyridines

Two bipyridine isomers (2,2'- and 4,4'-), used as coformers and ligands in coordination chemistry, were subjected to solid form screening and crystal structure prediction. One anhydrate and a formic acid disolvate were crystallized for 2,2'-bipyridine, whereas multiple solid-state forms, anhydrate, dihydrate, and eight solvates with carboxylic acids, including a polymorphic acetic acid disolvate, were found for the 4,4'-isomer. Seven of the solvates are reported for the first time, and structural information is provided for six of the new solvates. All twelve solid-state forms were investigated comprehensively using experimental [thermal analysis, isothermal calorimetry, X-ray diffraction, gravimetric moisture (de)sorption, and IR spectroscopy] and computational approaches. Lattice and interaction energy calculations confirmed the thermodynamic driving force for disolvate formation, mediated by the absence of H-bond donor groups of the host molecules. The exposed location of the N atoms in 4,4'-bipyridine facilitates the accommodation of bigger carboxylic acids and leads to higher conformational flexibility compared to 2,2'-bipyridine. For the 4,4'-bipyridine anhydrate ↔ hydrate interconversion hardly any hysteresis and a fast transformation kinetics are observed, with the critical relative humidity being at 35% at room temperature. The computed anhydrate crystal energy landscapes have the 2,2'-bipyridine as the lowest energy structure and the 4,4'-bipyridine among the low-energy structures and suggest a different crystallization behavior of the two compounds.

Synthesis and Characterization of a (-)-Epicatechin and Barbituric Acid Cocrystal: Single-Crystal X-ray Diffraction and Vibrational Spectroscopic Studies

The paper presents the contribution of the cocrystallization method in the physicochemical modification of catechins that exhibit low oral bioavailability. This was done to obtain cocrystals for two naturally occurring polyphenolic diastereoisomers (+)-catechin and (-)-epicatechin with commonly used coformers. Due to distinct crystallization behavior, only the (-)-epicatechin cocrystal with barbituric acid in a 1:1 stoichiometry was obtained. The cocrystal of (-)-epicatechin (EC) with barbituric acid (BTA) was prepared by the slow solvent-evaporation technique. The structure and intermolecular interactions were determined by X-ray crystallographic techniques. The analysis of packing and interactions in the crystal lattice revealed that molecules in the target cocrystal were packed into tapes, formed by the O-H···O type contacts between the (-)-epicatechin and coformer molecules. The EC molecules interact with the carboxyl group in the BTA coformer mainly by -OH groups from the benzene ring A. The cocrystalline phase constituents were also investigated in terms of Hirshfeld surfaces. The application of Raman spectroscopy confirmed the involvement of the C=O group in the formation of hydrogen bonds between the (-)-epicatechin and barbituric acid molecules. Additionally, the solubility studies of pure EC and the EC-BTA cocrystal exhibited minor enhancement of EC solubility in the buffer solution, and pH measurements confirmed a stable level of solubility for EC and its cocrystal.

Structural variety of heterosynthons in linezolid cocrystals with modified thermal properties

In a search for new crystalline forms of linezolid with modified thermal properties five cocrystals of this wide range antibiotic with aromatic acids were obtained via mechanochemical grinding and analyzed with single crystal X-ray diffraction, solid-state NMR spectroscopy, powder X-ray diffraction and DSC measurements. The coformers used in this study were benzoic acid, p-hydroxybenzoic acid, protocatechuic acid, γ-resorcylic acid and gallic acid. In each of the cocrystals distinct structural features have been found, including a variable amount of water and different heterosynthons, indicating that there is more than one type of intermolecular interaction preferred by the linezolid molecule. Basing on the frequency of the observed supramolecular synthons, the proposed hierarchy of the hydrogen-bond acceptor sites of linezolid (LIN) is C=O_amide > C=O_oxazolidone > C-O-C_morpholine > C-N-C_morpholine > C-O-C_oxazolidone. In addition, aromatic-aromatic interactions were found to be important in the stabilization of the analyzed structures. The obtained cocrystals show modified thermal properties, with four of them having melting points lower than the temperature of the phase transition from linezolid form II to linezolid form III. Such a change in this physicochemical property allows for the future application of melting-based techniques of introducing linezolid into drug delivery systems. In addition a change in water solubility of linezolid upon cocrystalization was evaluated, but only in the case of the cocrystal with protocatechuic acid was there a significant (43%) improvement in solubility in comparison with linezolid.

The Eight Hydrates of Strychnine Sulfate

Commercial samples of strychnine sulfate were used as the starting material in crystallization experiments accompanied by stability studies. Eight hydrate forms (HyA-HyG), including five novel hydrates, were verified. The crystal structures of HyA ("pentahydrate") and HyF ("hexahydrate") were determined from single-crystal X-ray diffraction data. HyF was identified as the most stable hydrate at high water activities at room temperature (RT), and HyA and HyC were also found to be stable at ambient conditions. Long-time storage experiments over nearly two decades confirm that these three hydrates are stable at ambient conditions (20-60% relative humidity). The other five hydrates, HyB ("dihydrate"), HyD, HyE, HyG, and HyH, are only observable at the low(est) relative humidity (RH) levels at RT. Some of these latter forms can only exist within a very narrow RH range and are therefore intermediate phases. By applying a range of complementary experimental techniques such as gravimetric moisture sorption analysis, thermal analysis, moisture controlled PXRD measurements, and variable temperature IR spectroscopy in combination with principal component analysis, it was possible to identify the distinct hydrate phases and elucidate their stability and dehydration pathways. The observed (de)hydration routes, HyA ↔ HyB, HyC ↔ HyD ↔ HyE, HyF ↔ HyG ↔ HyH and HyF → HyA ↔ HyB, depended on the initial hydrate form, particle size, and atmospheric conditions. In addition, a transformation from HyC/HyA to HyF occurs at high RH values at RT. The specific moisture and temperature conditions of none of the applied drying regimes yielded a crystalline water-free form, which highlights the essential role of water molecules for the formation and stability of the crystalline strychnine sulfate phases.

Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z' = 1 polymorph (form II), crystallize in P2₁/c and P1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z' = 2 polymorph. In addition, cases of serendipitous agreement in terms of ¹H or ¹³C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Geometric landscapes for material discovery within energy-structure-function maps

Porous molecular crystals are an emerging class of porous materials formed by crystallisation of molecules with weak intermolecular interactions, which distinguishes them from extended nanoporous materials like metal-organic frameworks (MOFs). To aid discovery of porous molecular crystals for desired applications, energy-structure-function (ESF) maps were developed that combine a priori prediction of both the crystal structure and its functional properties. However, it is a challenge to represent the high-dimensional structural and functional landscapes of an ESF map and to identify energetically favourable and functionally interesting polymorphs among the 1000s to 10 000s of structures typically on a single ESF map. Here, we introduce geometric landscapes, a representation for ESF maps based on geometric similarity, quantified by persistent homology. We show that this representation allows the exploration of complex ESF maps, automatically pinpointing interesting crystalline phases available to the molecule. Furthermore, we show that geometric landscapes can serve as an accountable descriptor for porous materials to predict their performance for gas adsorption applications. A machine learning model trained using this geometric similarity could reach a remarkable accuracy in predicting the materials' performance for methane storage applications.

Crystal structure determination of an elusive methanol solvate – hydrate of catechin using crystal structure prediction and NMR crystallography

A useful short-cut was developed to limit the number of molecular conformations that need to be regarded in crystal structure prediction calculations, which led to the crystal structure determination of new methanol solvate – hydrate of catechin.

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.

Experimental and computational approaches to produce and characterise isostructural solvates

A combination of experiment and theory was applied to rationalise the formation, stability and phase transitions of isostructural dapsone hemisolvates. Critical solvent properties as well as structural and energetic features are discussed.