Co-crystal Prediction by Artificial Neural Networks*.

A significant amount of attention has been given to the design and synthesis of co-crystals by both industry and academia because of its potential to change a molecule's physicochemical properties. Yet, difficulties arise when searching for adequate combinations of molecules (or coformers) to form co-crystals, hampering the efficient exploration of the target's solid-state landscape. This paper reports on the application of a data-driven co-crystal prediction method based on two types of artificial neural network models and co-crystal data present in the Cambridge Structural Database. The models accept pairs of coformers and predict whether a co-crystal is likely to form. By combining the output of multiple models of both types, our approach shows to have excellent performance on the proposed co-crystal training and validation sets, and has an estimated accuracy of 80 % for molecules for which previous co-crystallization data is unavailable.

The Crystalline Sponge Method in Water.

The crystalline sponge method entails the elucidation of the (absolute) structure of molecules from a solution phase using single-crystal X-ray diffraction and eliminates the need for crystals of the target compound. An important limitation for the application of the crystalline sponge method is the instability of the available crystalline sponges that can act as host crystals. The host crystal that is most often used decomposes in protic or nucleophilic solvents, or when guest molecules with Lewis basic substituents are introduced. Here a new class of (water) stable host crystals based on f-block metals is disclosed. It can be shown that these hosts not only increase the scope of the crystalline sponge method to a wider array of solvents and guests, but that they can even be applied to aqueous solutions containing hydrophilic guest molecules, thereby extending the crystalline sponge method to the important field of water-based chemistry.

Formal Synthesis of Solanoeclepin A: Enantioselective Allene Diboration and Intramolecular [2+2] Photocycloaddition for the Construction of the Tricyclic Core.

An enantioselective synthesis of an intermediate in the Tanino total synthesis of solanoeclepin A has been developed. The key step was an intramolecular [2+2] photocycloaddition, which led to the tricyclo[5.2.1.0(1, 6)] decane core in six steps. The first photosubstrate, prepared through an indium-mediated Barbier-type reaction, gave an excellent [2+2] cycloaddition, but it could not be obtained in sufficient enantiopurity. The second photosubstrate, prepared through an asymmetric allene diborylation in high enantiomeric excess, gave the [2+2] cycloaddition product in high yield on irradiation at 365 nm on 20 g scale in a flow system. Other important steps were the replacement of a boronate group at the quaternary carbon by a vinyl group and diastereoselective cyclopropanation of an allylic alcohol.

Stabilisation of 2,6-diarylpyridinium cation by through-space polar-π interactions.

The through-space polar-π interactions between pyridinium ion and the adjacent aromatic rings in 2,6-diarylpyridines affect the pKa values. Hammett analysis illustrates that the basicity of pyridines correlates well with the sigma values of the substituents at the para position of the flanking aryl rings.

Strong induced-fit binding of viologen and pyridine derivatives in adjustable porphyrin cavities.

The synthesis and binding properties of new porphyrin cage compounds consisting of a rigid diphenylglycoluril part, which is connected via flexible bis(ethyleneoxy) spacers to a (metallo)porphyrin "roof", are reported. Binding of viologen guests and pyridine ligands in these porphyrin cages are accompanied by significant conformational reorganizations of the hosts. Despite these structural changes, association constants are still very high, revealing that not only receptors that bind guests according to a lock-and-key mechanism but also those that bind guests by an induced-fit mechanism can exhibit strong binding.

Thermodynamics and kinetics of guest-induced switching between "basket handle" porphyrin isomers.

The synthesis and switching properties of two "basket handle" porphyrin isomers is described. The cis-oriented meso-phenyl groups of these porphyrins are linked at their ortho-positons via benzocrown-ether-based spacers, which as a result of slow atropisomerization are located either on the same side of the porphyrin plane (cis), or on opposite sides (trans). In solution, the cis-linked isomer slowly isomerizes in the direction of the thermodynamically more stable trans-isomer. In the presence of viologen (N,N'-dialkyl-4,4'-bipyridinium) derivatives, which have different affinities for the two isomers, the isomerization equilibrium could be significantly influenced. In addition, the presence of these guests was found to enhance the rate of the switching process, which was suggested to be caused by favorable interactions between the positively charged guest and the crown ethers of the receptor, stabilizing the transition state energies of the isomerization reaction between the two isomers.

Uncorrelated dynamical processes in tetranuclear carboxylate clusters studied by variable-temperature 1H NMR spectroscopy.

Tetranuclear carboxylate clusters with the general structural formula [M4(L)2(O2CR)4] (M = Cd, Zn; LH2 = 2,6-bis(1-(2-hydroxyphenyl)-iminoethyl)pyridine; R = CH3, C6H5) were studied by variable-temperature (VT) (1)H NMR spectroscopy. The dynamics of these clusters in solution can be described by two uncorrelated dynamical processes. The first dynamical process is the interconversion, both inter- as well as intramolecular, between syn-syn bridging and chelating carboxylate ligands. It is shown that this carboxylate interconversion mechanism is predominantly intramolecular for [Cd4(L)2(O2CCH3)4] (1a), whereas for [Zn4(L)2(O2CCH3)4] (2a) it is predominantly intermolecular. Two models for the second dynamic process, which involves the diiminepyridine ligand, are described. The first model comprises a nondissociative rotation around an internal axis, which changes the chirality of the cluster. The second model is based on the dissociation of the tetranuclear cluster into two dimeric species, which recombine again. This last model is supported by scrambling experiments between [Zn4(L)2(O2CCH3)4] (2a) and [Zn4(L3)2(O2CCH3)4] (5) (L3H2 = 2,6-bis(1-(2-hydroxyphenyl)-iminoethyl)4-chloropyridine).

Chemical, Biochemical, Cellular, and Physiological Characterization of Leucettinib-21, a Down Syndrome and Alzheimer's Disease Drug Candidate.

Leucettinibs are substituted 2-aminoimidazolin-4-ones (inspired by the marine sponge natural product Leucettamine B) developed as pharmacological inhibitors of DYRK1A (dual-specificity, tyrosine phosphorylation-regulated kinase 1A), a therapeutic target for indications such as Down syndrome and Alzheimer's disease. Leucettinib-21 was selected as a drug candidate following extensive structure/activity studies and multiparametric evaluations. We here report its physicochemical properties (X-ray powder diffraction, differential scanning calorimetry, stability, solubility, crystal structure) and drug-like profile. Leucettinib-21's selectivity (analyzed by radiometric, fluorescence, interaction, thermal shift, residence time assays) reveals DYRK1A as the first target but also some "off-targets" which may contribute to the drug's biological effects. Leucettinib-21 was cocrystallized with CLK1 and modeled in the DYRK1A structure. Leucettinib-21 inhibits DYRK1A in cells (demonstrated by direct catalytic activity and phosphorylation levels of Thr286-cyclin D1 or Thr212-Tau). Leucettinib-21 corrects memory disorders in the Down syndrome mouse model Ts65Dn and is now entering safety/tolerance phase 1 clinical trials.

Molecular recognition and self-assembly special feature: Squaring cooperative binding circles.

The cooperative binding effects of viologens and pyridines to a synthetic bivalent porphyrin receptor are used as a model system to study how the magnitudes of these effects relate to the experimentally obtained values. The full thermodynamic and kinetic circles concerning both activation and inhibition of the cage of the receptor for the binding of viologens were measured and evaluated. The results strongly emphasize the apparent character of measured binding and rate constants, in which the fractional saturation of receptors with other guests is linearly expressed in these constants. The presented method can be used as a simple tool to better analyze and comprehend the experimentally observed kinetics and thermodynamics of natural and artificial cooperative systems.

Comparing and Quantifying the Efficiency of Cocrystal Screening Methods for Praziquantel.

Pharmaceutical cocrystals are highly interesting due to their effect on physicochemical properties and their role in separation technologies, particularly for chiral molecules. Detection of new cocrystals is a challenge, and robust screening methods are required. As numerous techniques exist that differ in their crystallization mechanisms, their efficiencies depend on the coformers investigated. The most important parameters characterizing the methods are the (a) screenable coformer fraction, (b) coformer success rate, (c) ability to give several cocrystals per successful coformer, (d) identification of new stable phases, and (e) experimental convenience. Based on these parameters, we compare and quantify the performance of three methods: liquid-assisted grinding, solvent evaporation, and saturation temperature measurements of mixtures. These methods were used to screen 30 molecules, predicted by a network-based link prediction algorithm (described in Cryst. Growth Des. 2021, 21(6), 3428-3437) as potential coformers for the target molecule praziquantel. The solvent evaporation method presented more drawbacks than advantages, liquid-assisted grinding emerged as the most successful and the quickest, while saturation temperature measurements provided equally good results in a slower route yielding additional solubility information relevant for future screenings, single-crystal growth, and cocrystal production processes. Seventeen cocrystals were found, with 14 showing stability and 12 structures resolved.

Cocrystals of Praziquantel: Discovery by Network-Based Link Prediction.

Cocrystallization has been promoted as an attractive early development tool as it can change the physicochemical properties of a target compound and possibly enable the purification of single enantiomers from racemic compounds. In general, the identification of adequate cocrystallization candidates (or coformers) is troublesome and hampers the exploration of the solid-state landscape. For this reason, several computational tools have been introduced over the last two decades. In this study, cocrystals of Praziquantel (PZQ), an anthelmintic drug used to treat schistosomiasis, are predicted with network-based link prediction and experimentally explored. Single crystals of 12 experimental cocrystal indications were grown and subjected to a structural analysis with single-crystal X-ray diffraction. This case study illustrates the power of the link-prediction approach and its ability to suggest a diverse set of new coformer candidates for a target compound when starting from only a limited number of known cocrystals.

The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal 1H-NMR coupling constants.

The idopyranose ring plays a pivotal role in the conformational, dynamical, and intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate and it was early on assigned a role in the Sugar Code governing biological recognition processes. There is consensus that next to the two canonical 1C4 and 4C1 chair conformations, the conformational space accessible to the idopyranose ring entails a 2SO skew-boat conformation, but the equilibrium between these three ring puckers has evaded satisfactory quantification. In this study a meta-analysis of X-ray solid-state data and vicinal NMR coupling constants is presented, based on the Truncated Fourier Puckering (TFP) formalism and the generalized Karplus (CAGPLUS) equation. This approach yields a model-free, granular and consistent reckoning of 159 idopyranose solution puckering equilibria studied by NMR and allows us to reproduce the involved 636 NMR vicinal couplings with an overall residual RMS(Jobs-Jcalc) of 0.184 Hz. Our analyses show that for all ring systems examined, the idopyranosyl chair conformations take up the same ring pucker irrespective of the ring substituent pattern or a vast variety in experimental conditions. Instead, it is the (skew-)boat conformation that adapts to the substitution pattern of the idopyranose ring or a specific sulfation pattern of neighboring saccharides. All idopyranose rings are involved in conformational equilibria that subsume the aforementioned conformers which turn out to differ only a few kJ/mole in conformational energy. Thus, the plasticity and flexibility of idopyranose remains intact under practically all circumstances and, as the glycosidic linkages in heparin are considered to be relatively stiff, the iduronic moiety functions as the linchpin of heparin flexibility thereby being rather a "space(r)" than a "letter" in the alleged Sugar Code alphabet.

Ligand-controlled magnetic interactions in Mn(4) clusters.

A method is presented to design magnetic molecules in which the exchange interaction between adjacent metal ions is controlled by electron density withdrawal through their bridging ligands. We synthesized a novel Mn(4) cluster in which the choice of the bridging carboxylate ligands (acetate, benzoate, or trifluoroacetate) determines the type and strength of the three magnetic exchange couplings (J(1), J(2), and J(3)) present between the metal ions. Experimentally measured magnetic moments in high magnetic fields show that, upon electron density withdrawal, the main antiferromagnetic exchange constant J(1) decreases from -2.2 K for the [Mn(4)(OAc)(4)] cluster to -1.9 K for the [Mn(4)(H(5)C(6)COO)(4)] cluster and -0.6 K for the [Mn(4)(F(3)CCOO)(4)] cluster, while J(2) decreases from -1.1 K to nearly 0 K and J(3) changes to a small ferromagnetic coupling. These experimental results are further supported with density-functional theory calculations based on the obtained crystallographic structures of the [Mn(4)(OAc)(4)] and [Mn(4)(F(3)CCOO)(4)] clusters.

Cocrystals in the Cambridge Structural Database: a network approach.

To obtain a better understanding of which coformers to combine for the successful formation of a cocrystal, techniques from data mining and network science are used to analyze the data contained in the Cambridge Structural Database (CSD). A network of coformers is constructed based on cocrystal entries present in the CSD and its properties are analyzed. From this network, clusters of coformers with a similar tendency to form cocrystals are extracted. The popularity of the coformers in the CSD is unevenly distributed: a small group of coformers is responsible for most of the cocrystals, hence resulting in an inherently biased data set. The coformers in the network are found to behave primarily in a bipartite manner, demonstrating the importance of combining complementary coformers for successful cocrystallization. Based on our analysis, it is demonstrated that the CSD coformer network is a promising source of information for knowledge-based cocrystal prediction.

Enantioselective BINOL-phosphoric acid catalyzed Pictet-Spengler reactions of N-benzyltryptamine.

Optically active tetrahydro-beta-carbolines were synthesized via an ( R)-BINOL-phosphoric acid-catalyzed asymmetric Pictet-Spengler reaction of N-benzyltryptamine with a series of aromatic and aliphatic aldehydes. The tetrahydro-beta-carbolines were obtained in yields ranging from 77% to 97% and with ee values up to 87%. The triphenylsilyl-substituted BINOL-phosphoric acid proved to be the catalyst of choice for the reaction with aromatic aldehydes. For the aliphatic aldehydes, 3,5-bistrifluoromethylphenyl-substituted BINOL-phosphoric acid was identified as the best catalyst.

Fully orthogonally protected 2-deoxystreptamine from kanamycin.

A fully orthogonally protected and enantiopure 2-deoxystreptamine derivative is prepared in a few straightforward steps from commercially available kanamycin. Resolution of a sterically hindered diacetate was effected by a Verenium esterase and was followed by a chemoselective Staudinger reduction-acylation protocol.

Racemic and Enantiopure Camphene and Pinene Studied by the Crystalline Sponge Method.

The use of an achiral metal-organic framework for structure determination of chiral compounds is demonstrated for camphene and pinene. The structure of enantiopure ß-pinene can be resolved using the crystalline sponge method. However, α-pinene cannot be resolved using enantiopure material alone because no ordering of guest molecules takes place in that case. Interestingly, enantiomeric pairs order inside the channels of the host framework when impure (+)-camphene is offered to the host, which is also the case when a racemic mixture of α-pinene is used. A mixture of (+)-α-pinene and (-)-ß-pinene also leads to ordered incorporation in the host, showing the influence of the presence of an inversion center in the host framework. We further show that powder X-ray diffraction provides a direct view on incorporation of ordered guest molecules. This technique, therefore, provides a way to determine the optimal and/or minimal soaking time. In contrast, color change of the crystal only demonstrates guest uptake, not ordering. Moreover, we show that color change can also be caused by guest-induced host degradation.

Polymorphism and Modulation of Para-Substituted l-Phenylalanine.

The crystal structure of para-methyl-l-phenylalanine at 230 K resembles that of the para-fluorinated analogue from the literature but is commensurately modulated with seven molecules in the asymmetric unit (Z' = 7). At 100 K, the superstructure loses its modulation, leading to a unit cell with Z' = 1, with clear disorder in the phenyl ring orientations. The methyl-substituent in para-methyl-l-phenylalanine has, in contrast to fluorine, no polar interactions with protons of neighboring molecules, which might allow for the well-defined modulation of the crystal structure at 230 K.

Report on the sixth blind test of organic crystal structure prediction methods.

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

Diastereoselective synthesis of (2S,5R)-5-hydroxypipecolic acid and 6-substituted derivatives.

[reaction: see text] Herein, we report a diastereoselective synthesis of the natural product (2S,5R)-5-hydroxypipecolic acid and 6-substituted derivatives thereof. The key step in the synthetic sequence is a novel highly diastereoselective epoxidation reaction of an enantiomerically pure cyclic enamide intermediate.