Conformational polymorphism

A quantum crystallographic approach to short hydrogen bonds

In this work we use high-resolution synchrotron X-ray diffraction for electron density mapping, in conjunction with ab initio modelling, to study short O-H⋯O and O+-H⋯O- hydrogen bonds whose behaviour is known to be tuneable by temperature. The short hydrogen bonds have donor-acceptor distances in the region of 2.45 Å and are formed in substituted urea and organic acid molecular complexes of N,N'-dimethylurea oxalic acid 2 : 1 (1), N,N-dimethylurea 2,4-dinitrobenzoate 1 : 1 (2) and N,N-dimethylurea 3,5-dinitrobenzoic acid 2 : 2 (3). From the combined analyses, these complexes are found to fall within the salt-cocrystal continuum and exhibit short hydrogen bonds that can be characterised as both strong and electrostatic (1, 3) or very strong with a significant covalent contribution (2). An additional charge assisted component is found to be important in distinguishing the relatively uncommon O-H⋯O pseudo-covalent interaction from a typical strong hydrogen bond. The electron density is found to be sensitive to the extent of static proton transfer, presenting it as a useful parameter in the study of the salt-cocrystal continuum. From complementary calculated hydrogen atom potentials, we attribute changes in proton position to the molecular environment. Calculated potentials also show zero barrier to proton migration, forming an 'energy slide' between the donor and acceptor atoms. The better fundamental understanding of the short hydrogen bond in the 'zone of fluctuation' presented in a salt-cocrystal continuum, enabled by studies like this, provide greater insight into their related properties and can have implications in the regulation of pharmaceutical materials.

Crystalline Forms of Trazodone Dihydrates

In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water molecules, which are stabilised by the N4 acceptor atom of the piperazine ring and the pendant carbonyl O1 atom of the triazole ring, as well as other water molecules. The strong dipole moment expected for the O1 atom makes it a good hydrogen bond acceptor for stabilising the chains of water molecules. Each molecule of trazodone has a similar conformation in both hydrates, except for the propyl chains, which adopt different conformations: anti-gauche in the β hydrate (triazole N-C-C-C and C-C-C-piperazine N) and anti-anti in the γ hydrate. Both piperazine rings adopt chair conformations, and the exocyclic N-C bonds are in equatorial orientations. The Hirshfeld surfaces and two-dimensional fingerprint plots for the polymorphs were calculated using CrystalExplorer17, which indicated contacts significantly shorter than the sum of the van der Waals radii in the vicinity of the piperazine N4 and triazole O1 atoms corresponding to the strong hydrogen bonds accepted by these atoms.

Triglycine (GGG) Adopts a Polyproline II (pPII) Conformation in Its Hydrated Crystal Form: Revealing the Role of Water in Peptide Crystallization

Polyproline II (pPII) is a left-handed 31-helix conformation, which has been observed to be the most abundant secondary structure in unfolded peptides and proteins compared to α-helix and β-sheet. Although pPII has been reported as the most stable conformation for several unfolded short chain peptides in aqueous solution, it is rarely observed in their solid state. Here, we show for the first time a glycine homopeptide (gly-gly-gly) adopting the pPII conformation in its crystalline dihydrate structure. The single crystal X-ray structure with molecular dynamic simulation suggests that a network of water and the charged carboxylate group is critical in stabilizing the pPII conformation in solid state, offering an insight into the structures of unfolded regions of proteins and the role of water in peptide crystallization.

Tilt and shift polymorphism in molecular perovskites

Molecular perovskites, i.e. ABX₃ coordination polymers with a perovskite structure, are a chemically diverse material platform for studying fundamental and applied materials properties such as barocalorics and improper ferroelectrics. Compared to inorganic perovskites, the use of molecular ions on the A- and X-site of molecular perovskites leads to new geometric and structural degrees of freedom. In this work we introduce the concept of tilt and shift polymorphism, categorising irreversible perovskite-to-perovskite phase transitions in molecular perovskites. As a model example we study the new molecular perovskite series [(nPr)₃(CH₃)N]M(C₂N₃)₃ with M = Mn²⁺, Co²⁺, Ni²⁺, and nPr = n-propyl, where different polymorphs crystallise in the perovskite structure but with different tilt systems depending on the synthetic conditions. Tilt and shift polymorphism is a direct ramification of the use of molecular building units in molecular perovskites and as such is unknown for inorganic perovskites. Given the role of polymorphism in materials science, medicine and mineralogy, and more generally the relation between physicochemical properties and structure, the concept introduced herein represents an important step in classifying the crystal chemistry of molecular perovskites and in maturing the field.

Spectroscopic Identification of Hydrogen Bond Vibrations and Quasi-Isostructural Polymorphism in N-Salicylideneaniline

The ortho-hydroxy aryl Schiff base 2-[(E)-(phenylimino)methyl]phenol and its deutero-derivative have been studied by the inelastic incoherent neutron scattering (IINS), infrared (IR) and Raman experimental methods, as well as by Density Functional Theory (DFT) and Density-Functional Perturbation Theory (DFPT) simulations. The assignments of vibrational modes within the 3500–50 cm⁻¹ spectral region made it possible to state that the strong hydrogen bond in the studied compound can be classified as the so-called quasi-aromatic bond. The isotopic substitution supplemented by the results of DFT calculations allowed us to identify vibrational bands associated with all five major hydrogen bond vibrations. Quasi-isostructural polymorphism of 2-[(E)-(phenylimino)methyl]phenol (SA) and 2-[(E)-(phenyl-D₅-imino)methyl]phenol (SA-C₆D₅) has been studied by powder X-ray diffraction in the 20–320 K temperature range.

Real-Time Fluorescence Visualization of Nanoparticle Aggregation and the Polymorph-Transition Process of a Mechanofluorochromic Difluoroboron-β-Diketone Derivative

The use of organic nanomaterials in biomedical and optical devices has been widely studied. The key to improving the performance and stability of these devices is to control the fabrication process, which determines the phase stability and photophysical properties. In this study, fluorescence changes were observed during the reprecipitation process of mechanofluorochromic molecules of dibenzoyl(methanato)boron difluoride. The cyan-emission phase (C-phase) was first identified. The time evolution of the resolved fluorescence spectra revealed that the green-emission phase (G-phase) was formed from the amorphous phase with yellow emission via the C-phase, in addition to the direct formation of the G-phase. Combined with the results of the investigation into the thermal properties, the fluorescence changes clearly indicate a two-step nucleation process and Ostwald's rule of stages for polymorph transition, which enables us to not only provide guidance for controlling the fabrication process but also propose the ripening process for organic nanoparticle formation.

Selective Crystallization of d-Mannitol Polymorphs Using Surfactant Self-Assembly

Selective crystallization of polymorphs is highly sought after in industrial practice. Yet, state-of-the-art techniques either use laboriously engineered solid surfaces or strenuously prepared heteronucleants. We propose an approach where surfactants in solution self-assemble effortlessly into mesoscopic structures dictating the polymorphic outcome of the target solute. Sodium dodecyl sulfate (SDS) surfactant is used as a tailored additive to crystallize different polymorphic forms of a model active pharmaceutical ingredient, d-mannitol. Different mesoscopic phases of SDS template particular polymorphs: packed monolayers, micelles, and crystals favored the β, α, and δ forms of d-mannitol, respectively. A synergistic effect of topological templating and molecular interactions is proposed as the rationale behind the observed selective crystallization of polymorphs. This crystal engineering technique suggests that surfactant self-assemblies can be used as tailored templates for polymorphic control.

Polymorphism and Conformational Equilibrium of Nitro-Acetophenone in Solid State and under Matrix Conditions

Conformational and polymorphic states in the nitro-derivative of o-hydroxy acetophenone have been studied by experimental and theoretical methods. The potential energy curves for the rotation of the nitro group and isomerization of the hydroxyl group have been calculated by density functional theory (DFT) to estimate the barriers of the conformational changes. Two polymorphic forms of the studied compound were obtained by the slow and fast evaporation of polar and non-polar solutions, respectively. Both of the polymorphs were investigated by Infrared-Red (IR) and Raman spectroscopy, Incoherent Inelastic Neutron Scattering (IINS), X-ray diffraction, nuclear quadrupole resonance spectroscopy (NQR), differential scanning calorimetry (DSC) and density functional theory (DFT) methods. In one of the polymorphs, the existence of a phase transition was shown. The position of the nitro group and its impact on the crystal cell of the studied compound were analyzed. The conformational equilibrium determined by the reorientation of the hydroxyl group was observed under argon matrix isolation. An analysis of vibrational spectra was achieved for the interpretation of conformational equilibrium. The infrared spectra were measured in a wide temperature range to reveal the spectral bands that were the most sensitive to the phase transition and conformational equilibrium. The results showed the interrelations between intramolecular processes and macroscopic phenomena in the studied compound.

Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering

We present a systematic approach for the identification of statistically relevant conformational macrostates of organic molecules from molecular dynamics trajectories. The approach applies to molecules characterized by an arbitrary number of torsional degrees of freedom and enables the transferability of the macrostates definition across different environments. We formulate a dissimilarity measure between molecular configurations that incorporates information on the characteristic energetic cost associated with transitions along all relevant torsional degrees of freedom. Such metric is employed to perform unsupervised clustering of molecular configurations based on the Fast Search and Find of Density Peaks algorithm. We apply this method to investigate the equilibrium conformational ensemble of Sildenafil, a conformationally complex pharmaceutical compound, in different environments including the crystal bulk, the gas phase, and three different solvents (acetonitrile, 1-butanol, and toluene). We demonstrate that while Sildenafil can adopt more than 100 metastable conformational configurations, only 12 are significantly populated across all of the environments investigated. Despite the complexity of the conformational space, we find that the most abundant conformers in solution are the closest to the conformers found in the most common Sildenafil crystal phase.

Crystal Structure Prediction Methods for Organic Molecules: State of the Art

The prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.

Reversible polymorphic structural transition of crown-like nickel nanoclusters and its effect on conductivity

We report the reversible polymorphic phase transition of [Ni6(PET)12] (PET = phenylethanethiol) and its effect on the conductivity. This cluster's self-assembly leads to two polymorphic structures with distinct conductivity, caused by variation of the non-covalent SS interactions. These results enlighten the effect of non-covalent interactions on conductivity.

Taming Radical Pairs in the Crystalline Solid State: Discovery and Total Synthesis of Psychotriadine

Solid-state photodecarbonylation is an attractive but underutilized methodology to forge hindered C-C bonds in complex molecules. This study discloses the use of this reaction to assemble the vicinal quaternary stereocenter motif present in bis(cyclotryptamine) alkaloids. Our strategy was enabled by experimental and computational investigations of the role of substrate conformation on the success or failure of the solid-state photodecarbonylation reaction. This informed a crystal engineering strategy to optimize the key step of the total synthesis. Ultimately, this endeavor culminated in the successful synthesis of the bis(cyclotryptamine) alkaloid "psychotriadine," which features the elusive piperidinoindoline framework. Psychotriadine, a previously unknown compound, was identified in the extracts of the flower Psychotria colorata, suggesting it is a naturally occurring metabolite.

Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series

Drug design with patient centricity for ease of administration and pill burden requires robust understanding of the impact of chemical modifications on relevant physicochemical properties early in lead optimization. To this end, we have developed a physics-based ensemble approach to predict aqueous thermodynamic crystalline solubility, with a 2D chemical structure as the input. Predictions for the bromodomain and extraterminal domain (BET) inhibitor series show very close match (0.5 log unit) with measured thermodynamic solubility for cases with low crystal anisotropy and good match (1 log unit) for high anisotropy structures. The importance of thermodynamic solubility is clearly demonstrated by up to a 4 log unit drop in solubility compared to kinetic (amorphous) solubility in some cases and implications thereof, for instance on human dose. We have also demonstrated that incorporating predicted crystal structures in thermodynamic solubility prediction is necessary to differentiate (up to 4 log unit) between solubility of molecules within the series. Finally, our physics-based ensemble approach provides valuable structural insights into the origins of 3-D conformational landscapes, crystal polymorphism, and anisotropy that can be leveraged for both drug design and development.

A Design Principle for Polar Assemblies with C3 -Sym Bowl-Shaped π-Conjugated Molecules

Polar materials attract wide research interest due to their unique properties, such as ferroelectricity and the bulk photovoltaic effect (BPVE), which are not accessible with nonpolar materials. However, in general, rationally designing polar materials is difficult because nonpolar materials are more favorable in terms of dipole-dipole interactions. Here, we report a rational strategy to form polar assemblies with bowl-shaped π-conjugated molecules and a molecular design principle for this strategy. We synthesized and thoroughly characterized 12 single crystals with the help of various theoretical calculations. Furthermore, we demonstrated that it can be possible to predict whether polar assemblies become more favorable or not by estimating their lattice energies. We believe that this study contributes to the development of organic polar materials and their related studies.

Tuning the mechanical flexibility of organic molecular crystals by polymorphism for flexible optical waveguides

The ability to selectively tune the optical and the mechanical properties of organic molecular crystals offers a promising approach towards developing flexible optical devices.

Reversible facile single-crystal-to-single-crystal polymorphic transition accompanied by unit cell volume expansion and twinning

Reversible and facile single-crystal-to-single-crystal transformation between two polymorphs of diphenhydramine citrate leads to molecular level understanding of crystal phase change.

Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

Understanding the planar conformations in diarylsubstituted heteroarenes: structural and theoretical insights

We have synthesized and X-ray characterized a series of six diaryl-substituted heteroarenes in order to analyze unconventional intramolecular C_Ar–H⋯N/O in comparison to conventional H-bonds.

Conformational switch in the crystal states of a calix[4]arene

Two distinct conformational switches were observed in the crystals of calix[4]arene molecule: closed-I crystals transform to the open polymorph spontaneously; temperature induced reversible transformation of closed-I to a closed-II polymorph.

Conformational polymorphs of 3-cyclopropyl-5-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-7-yl)-1,2,4-oxadiazole

The dipharmacophore compound 3-cyclopropyl-5-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-7-yl)-1,2,4-oxadiazole, C₁₂H₁₁N₅O, was studied on the assumption of its potential biological activity. Two polymorphic forms differ in both their molecular and crystal structures. The monoclinic polymorphic form was crystallized from more volatile solvents and contains a conformer with a higher relative energy. The basic molecule forms an abundance of interactions with relatively close energies. The orthorhombic polymorph was crystallized very slowly from isoamyl alcohol and contains a conformer with a much lower energy. The basic molecule forms two strong interactions and a large number of weak interactions. Stacking interactions of the `head-to-head' type in the monoclinic structure and of the `head-to-tail' type in the orthorhombic structure proved to be the strongest and form stacked columns in the two polymorphs. The main structural motif of the monoclinic structure is a double column where two stacked columns interact through weak C-H...N hydrogen bonds and dispersive interactions. In the orthorhombic structure, a single stacked column is the main structural motif. Periodic calculations confirmed that the orthorhombic structure obtained by slow evaporation has a lower lattice energy (0.97 kcal mol^-1) compared to the monoclinic structure.

Features of the conformation of galunisertib molecules in the crystal structures of its solvates

A comparison of galunisertib in crystal structures of pure polymorphs and solvates enables studying the effects of solvate molecules on galunisertib conformations and highlights the features of realized noncovalent interactions.

Hydrates of adenosine 3′,5′-cyclic monophosphate sodium and their transformation

The difference of crystal water behaviors for cAMPNa hydrates was attributed mainly to the steric effects in lattices. Excessive loss of crystal water would destroy the host structure, and result in the disability of reversible transformation.

Structure prediction of crystals, surfaces and nanoparticles

We review the current techniques used in the prediction of crystal structures and their surfaces and of the structures of nanoparticles. The main classes of search algorithm and energy function are summarized, and we discuss the growing role of methods based on machine learning. We illustrate the current status of the field with examples taken from metallic, inorganic and organic systems. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.

Two conformational polymorphs of 4-methylhippuric acid

4-Methylhippuric acid {systematic name: 2-[(4-methylbenzoyl)amino]ethanoic acid}, a p-xylene excreted metabolite with a backbone containing three rotatable bonds (R-bonds), is likely to produce more than one stable molecular structure in the solid state. In this work, we prepared polymorph I by slow solvent evaporation (plates with Z' = 1) and polymorph II by mechanical grinding (plates with Z' = 2). Potential energy surface (PES) analysis, rotating the molecule about the C-C-N-C torsion angle, shows four conformational energy basins. The second basin, with torsion angles near -73°, agree with the conformations adopted by polymorph I and molecules A of polymorph II, and the third basin at 57° matched molecules B of polymorph II. The energy barrier between these basins is 27.5 kJ mol^-1. Superposition of the molecules of polymorphs I and II rendered a maximum r.m.s. deviation of 0.398 Å. Polymorphs I and II are therefore true conformational polymorphs. The crystal packing of polymorph I consists of C(5) chains linked by N-H...O interactions along the a axis and C(7) chains linked by O-H...O interactions along the b axis. In polymorph II, two molecules (A with A or B with B) are connected by two acid-amide O-H...O interactions rendering R₂²(14) centrosymmetric dimers. These dimers alternate to pile up along the b axis linked by N-H...O interactions. A Hirshfeld surface analysis localized weaker noncovalent interactions, C-H...O and C-H...π, with contact distances close to the sum of the van der Waals radii. Electron density at a local level using the Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization Function (ELF), or a semi-local level using noncovalent interactions, was used to rank interactions. Strong closed shell interactions in classical O-H...O and N-H...O hydrogen bonds have electron density highly localized on bond critical points. Weaker delocalized electron density is seen around the p-methylphenyl rings associated with dispersive C-H...π and H...H interactions.

Simulation and Assignment of the Terahertz Vibrational Spectra of Enalapril Maleate Cocrystal Polymorphs

The identification of crystalline drug polymorphs using terahertz vibrational spectroscopy is a powerful approach for the nondestructive and noninvasive characterization of solid-state pharmaceuticals. However, a complete understanding of the terahertz spectra of molecular solids is challenging to obtain because of the complex nature of the low-frequency vibrational motions found in the sub-3 THz (sub-100 cm^-1) range. Unambiguous assignments of the observed spectral features can be achieved through quantum mechanical solid-state simulations of crystal structures and lattice vibrations utilizing the periodic boundary condition approach. The terahertz spectra of two polymorphs of enalapril maleate are presented here to demonstrate that even large pharmaceuticals can be successfully modeled using solid-state density functional theory, including cocrystalline solids comprised of multiple distinct species. These simulations enable spectral assignments to be made, but also provide insights into the conformational and cohesion energies that contribute to the polymorph stabilities. The results reveal that the Form II polymorph of enalapril maleate is the more stable of the two under ambient conditions, and that this stability is driven by a greater intermolecular cohesion energy as compared to Form I.

X-ray structure of an unusual glycoluril derivative conformation: Structural analysis and influencing factors

The synthesis and X-ray structure of a novel glycoluril derivative are described. The crystal of the glycoluril derivative is obtained by slow evaporation in a refrigerator at about 5 °C. X-ray crystallographic analysis revealed that the compound crystallized in an unusual as conformation instead of the usual clip-shaped aa conformation. Structural analysis shows that the solvation effect, hydrogen bonding, and space-occupying effect influenced the crystallization conformation of the derivative. The X-ray crystallographic analysis in this work provides additional crystallographic evidence of the as conformation of the 3U glycoluril derivative and shows the effect of solvent water on the conformational behavior.

Can molecular flexibility control crystallization? The case of para substituted benzoic acids

Despite the technological importance of crystallization from solutions almost nothing is known about the relationship between the kinetic process of nucleation and the molecular and crystal structures of a crystallizing solute. Nowhere is this more apparent than in our attempts to understand the behavior of increasingly large, flexible molecules developed as active components in the pharmaceutical arena. In our current contribution we develop a general protocol involving a combination of computation (conformation analysis, lattice energy), and experiment (measurement of nucleation rates), and show how significant advances can be made. We present the first systematic study aimed at quantifying the impact of molecular flexibility on nucleation kinetics. The nucleation rates of 4 para substituted benzoic acids are compared, two of which have substituents with flexible chains. In making this comparison, the importance of normalizing data to account for differing solubilities is highlighted. These data have allowed us to go beyond popular qualitative descriptors such ‘crystallizability’ or ‘crystallization propensity’ in favour of more precise nucleation rate data. Overall, this leads to definite conclusions as to the relative importance of solution chemistry, solid-state interactions and conformational flexibility in the crystallization of these molecules and confirms the key role of intermolecular stacking interactions in determining relative nucleation rates. In a more general sense, conclusions are drawn as to conditions under which conformational change may become rate determining during a crystallization process.

Little is known about the relationship between the kinetic process of nucleation and the molecular and crystal structures of a crystallizing solute. Here we compare the behaviour of a series of benzoic acids with a focus on conformational effects.

Rich polymorphism in nicotinamide revealed by melt crystallization and crystal structure prediction

Overprediction is a major limitation of current crystal structure prediction (CSP) methods. It is difficult to determine whether computer-predicted polymorphic structures are artefacts of the calculation model or are polymorphs that have not yet been found. Here, we reported the well-known vitamin nicotinamide (NIC) to be a highly polymorphic compound with nine solved single-crystal structures determined by performing melt crystallization. A CSP calculation successfully identifies all six Z' = 1 and 2 experimental structures, five of which defy 66 years of attempts at being explored using solution crystallization. Our study demonstrates that when combined with our strategy for cultivating single crystals from melt microdroplets, melt crystallization has turned out to be an efficient tool for exploring polymorphic landscapes to better understand polymorphic crystallization and to more effectively test the accuracy of theoretical predictions, especially in regions inaccessible by solution crystallization.

Observation of crystallisation dynamics by crystal-structure-sensitive room-temperature phosphorescence from Au(I) complexes

The aggregation behaviour of Au(I) complexes in condensed phases can affect their emission properties. Herein, aggregation-induced room-temperature phosphorescence (RTP) is observed from the crystals of trinuclear Au(I) complexes. The RTP is highly sensitive to the crystal structure, with a slight difference in the alkyl side chains causing not only a change in the crystal structure but also a shift in the RTP maximum. Furthermore, in nanocrystals, reversible RTP colour changes are induced by phase transitions between crystal polymorphs during crystal growth from solution or the pulverisation of bulk crystals. The colour change mechanism is discussed in terms of intermolecular interactions in the crystal structure of the luminescent aggregates. The results suggest that the behaviour in nanocrystals may differ from that in bulk crystals. These insights will advance the fundamental understanding of crystallisation mechanisms and may aid in the discovery of new materials properties for solids with nano- to micrometre sizes.

ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules

Conformational equilibria are at the heart of drug design, yet their energetic description is often hampered by the insufficient accuracy of low-cost methods. Here we present a flexible and semi-automatic workflow based on quantum chemistry, ReSCoSS, designed to identify relevant conformers and predict their equilibria across different solvent environments in the Conductor-like Screening Model for Real Solvents (COSMO-RS) framework. We demonstrate the utility and accuracy of the workflow through conformational case studies on several drug-like molecules from literature where relevant conformations are known. We further show that including ReSCoSS conformers significantly improves COSMO-RS based predictions of physicochemical properties over single-conformation approaches. ReSCoSS has found broad adoption in the in-house drug discovery and development work streams and has contributed to establishing quantum-chemistry methods as a strategic pillar in ligand discovery.

Concomitant polymorphic forms of 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole

The dipharmacophore compound 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole, C10H11N5O, was studied on the assumption of its potential biological activity. Two concomitant polymorphs were obtained on crystallization from isopropanol solution and these were thoroughly studied. Identical conformations of the molecules are found in both structures despite the low difference in energy between the four possible conformers. The two polymorphs differ crucially with respect to their crystal structures. A centrosymmetric dimer formed due to both stacking interactions of the `head-to-tail' type and N—H...N(π) hydrogen bonds is the building unit in the triclinic structure. The dimeric building units form an isotropic packing. In the orthorhombic polymorphic structure, the molecules form stacking interactions of the `head-to-head' type, which results in their organization in a column as the primary basic structural motif. The formation of N—H...N(lone pair) hydrogen bonds between two neighbouring columns allows the formation of a double column as the main structural motif. The correct packing motifs in the two polymorphs could not be identified without calculations of the pairwise interaction energies. The triclinic structure has a higher density and a lower (by 0.60 kcal mol−1) lattice energy according to periodic calculations compared to the orthorhombic structure. This allows us to presume that the triclinic form of 3-cyclopropyl-5-(2-hydrazinylpyridin-3-yl)-1,2,4-oxadiazole is the more stable.

Encapsulated Nanodroplet Crystallization of Organic-Soluble Small Molecules

Single-crystal X-ray diffraction analysis (SCXRD) constitutes a universal approach for the elucidation of molecular structure and the study of crystalline forms. However, the discovery of viable crystallization conditions remains both experimentally challenging and resource intensive in both time and the quantity of analyte(s). We report a robot-assisted, high-throughput method for the crystallization of organic-soluble small molecules in which we employ only micrograms of analyte per experiment. This allows hundreds of crystallization conditions to be screened in parallel with minimal overall sample requirements. Crystals suitable for SCXRD are grown from nanoliter droplets of a solution of analyte in organic solvent(s), each of which is encapsulated within an inert oil to control the rate of solvent loss. This encapsulated nanodroplet crystallization methodology can also be used to search for new crystal forms, as exemplified through both our discovery of a new (13^th) polymorph of the olanzapine precursor ROY and SCXRD analysis of the “uncrystallizable” agrochemical dithianon.

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Single crystals of small molecules are grown from nanoscale droplets of organic solvent

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Discovery of the 13^th polymorph (R18) of olanzapine precursor ROY

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X-ray diffraction analysis of “uncrystallizable” agrochemical dithianon

Small molecules can form crystalline solids, in which individual molecules pack together into ordered three-dimensional arrays. Once a suitable crystal is grown, the packing and atomic connectivity of the constituent molecules can be studied by X-ray diffraction. However, the discovery of experimental conditions for successful crystal growth is often challenging. We have developed a nanoscale crystallization technique for organic-soluble small molecules by using high-throughput liquid-handling robotics to undertake multiple crystallization experiments simultaneously with minimal sample requirements and high success rates. We showcase our methodology through the crystallization of a diverse set of small molecules, including “uncrystallizables,” combined with structural analysis by X-ray diffraction. We anticipate that this rapid and reliable method for small-molecule crystallization will have far-reaching impact, facilitating academic and industrial research in the molecular sciences.

Molecular conformational evolution mechanism during nucleation of crystals in solution

Nucleation of crystals from solution is fundamental to many natural and industrial processes. In this work, the molecular mechanism of conformational polymorphism nucleation and the links between the molecular conformation in solutions and in crystals were investigated in detail by using 5-nitro-furazone as the model compound. Different polymorphs were prepared, and the conformations in solutions obtained by dissolving different polymorphs were analysed and compared. The solutions of 5-nitro-furazone were proven to contain multiple conformers through quantum chemical computation, Raman spectra analysis, 2D nuclear Overhauser effect spectroscopy spectra analysis and molecular dynamics simulation. The conformational evolution and desolvation path was illustrated according to the 1H NMR spectra of solutions with different concentrations. Finally, based on all the above analysis, the molecular conformational evolution path during nucleation of 5-nitro-furazone was illustrated. The results presented in this work shed a new light on the molecular mechanism of conformational polymorphism nucleation in solution.

Probing the structural pathway of conformational polymorph nucleation by comparing a series of α,ω-alkanedicarboxylic acids

Herein the nucleation pathway of conformational polymorphs was revealed by studying the relationships and distinctions among a series of α,ω-alkanedicarboxylic acids [HOOC-(CH2) n-2-COOH, named DAn, where n = 5, 7, 9, 11, 13, 15] in the solid state and in solution. Their polymorphic outcomes, with the exception of DA5, show solvent dependence: form I with conformation I crystallizes from solvents with hydrogen-bond donating (HBD) ability, whereas form II with conformation II crystallizes preferentially from solvents with no HBD ability. In contrast, form II of DA5 does not crystallize in any of the solvents used. Quantum mechanical computation showed that there is no direct conformational link between the solvents and the resultant polymorphic outcomes. Surprisingly, solute aggregates were found in no-HBD solvents by Fourier transform infrared spectroscopy, and only monomers could be detected in HBD solvents, suggesting stronger solvation. Furthermore, it was found that all six compounds including DA5 followed the same pattern in solution. Moreover, crystal-packing efficiency calculations and stability tests stated that dimorphs of DA5 bear a greater stability difference than others. These suggest that the rearrangement from conformation II to I could not be limited by hard desolvation in HBD solvents, where form I was also obtained. In other systems, metastable II was produced in the same solvents, probably as a result of the rearrangement being limited by hard desolvation. In this work, a comparative study uncovers the proposed nucleation pathway: difficulty in desolvation has a remarkable effect on the result of rearrangement and nucleation outcome.