Advanced crystallisation methods for small organic molecules

Molecular materials based on small organic molecules often require advanced structural analysis, beyond the capability of spectroscopic techniques, to fully characterise them. In such cases, diffraction methods such as single crystal X-ray diffraction (SCXRD), are one of the most powerful tools available to researchers, providing molecular and structural elucidation at atomic level resolution, including absolute stereochemistry. However SCXRD, and related diffraction methods, are heavily dependent on the availability of suitable, high-quality crystals, thus crystallisation often becomes the major bottleneck in preparing samples. Following a summary of classical methods for the crystallisation of small organic molecules, this review will focus on a number of recently developed advanced methods for crystalline material sample preparation for SCXRD. This review will cover two main areas of modern small organic molecule crystallisation, namely the inclusion of molecules within host complexes (e.g., "crystalline sponge" and tetraaryladamantane based inclusion chaperones) and the use of high-throughput crystallisation, employing "under-oil" approaches (e.g., microbatch under-oil and ENaCt). Representative examples have been included for each technique, together with a discussion of their relative advantages and limitations to aid the reader in selecting the most appropriate technique to overcome a specific analytical challenge.

Zn2+-Schiff's Base Complex as an "On-Off-On" Molecular Switch and a Fluorescence Probe for Cu2+ and Ag+ Ions

The present study presents a thorough theoretical analysis of the electronic structure and conformational preference of Schiff's base ligand N,N-bis(2-hydroxybenzilidene)-2,4,6-trimethyl benzene-1,3-diamine (H₂L) and its metal complexes with Zn²⁺, Cu²⁺ and Ag⁺ ions. This study aims to investigate the behavior of H₂L and the binuclear Zn²⁺ complex (1) as fluorescent probes for the detection of metal ions (Zn²⁺, Cu²⁺ and Ag⁺) using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The six conformers of the H₂L ligand were optimized using the B3LYP/6-311 +  + G** level of theory, while the L^-2-metal complexes were optimized by applying the B3LYP functional with the LANL2DZ/6-311 +  + G** mixed basis set. The gas-phase and solvated Enol-cis isomer (E-cis) was found to be the most stable species. The absorption spectra of the E-cis isomer and its metal complexes were simulated using B3LYP, CAM-B3LYP, M06-2X and ωB97X functionals with a 6-311 +  + G** basis set for C, O, N and H atoms and a LANL2DZ basis set for the metal ions (Zn²⁺, Cu²⁺ and Ag⁺). The computational results of the B3LYP functional were in excellent agreement with the experimental results. Hence, it was adopted for performing the emission calculations. The results indicated that metal complex (1) can act as a fluorescent chemosensor for the detection of Ag⁺ and Cu²⁺ ions through the mechanism of intermolecular charge transfer (ICT) and as a molecular switch "On-Off-On" via the replacement of Cu²⁺ by Ag⁺ ions, as proved experimentally.

The role of thermodynamically stable configuration in enhancing crystallographic diffraction quality of flexible MOFs

Single-crystal X-ray diffraction (SCXRD) is a widely used method for structural characterization. Generally, low temperature is of great significance for improving the crystallographic diffraction quality. Herein we observe that this practice is not always effective for flexible metal-organic frameworks (f-MOFs). An abnormal crystallography, that is, more diffraction spots at a high angle and better resolution of diffraction data as the temperature increases in the f-MOF (1-g), is observed. XRD results reveal that 1-g has a reversible anisotropic thermal expansion behavior with a record-high c-axial positive expansion coefficient of 1,401.8 × 10-6 K-1. Calculation results indicate that the framework of 1-g has a more stable thermodynamic configuration as the temperature increases. Such configuration has lower-frequency vibration and may play a key role in promoting higher Bragg diffraction quality at room temperature. This work is of great significance for how to obtain high-quality SCXRD diffraction data.

Low temperature insights into the crystal and magnetic structure of a neutral radical ferromagnet

The crystal structure of the radical ferromagnet 1a at 2 K reveals a contraction in the unit cell c constant which, at the molecular level, translates into a decrease in slippage of the radical π-stacks and an increase in ferromagnetic exchange interactions along the stacking axis. The results of BS-DFT calculations using long-range corrected functionals are consistent with an overall ferromagnetic topology.

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.

Advanced X-ray Shielding Materials Enabled by the Coordination of Well-Dispersed High Atomic Number Elements in Natural Leather

Nowadays, X-rays are playing increasingly important roles in daily life and industrial manufacture, which calls for effective and mobile shielding materials. However, it seems to be a paradox to prepare shielding materials simultaneously achieving excellent X-ray attenuation properties and superior mechanical strength. Here, an advanced leather-based X-ray shielding material containing bismuth and iodine (BiINP-LM) is prepared, and the stable and well-dispersed loading of high-Z element components is enabled by favorable interactions between bismuth iodide and leather, i.e., coordination, hydrogen bonds, and electrostatic attractions. A piece of BiINP-LM with 1.00 mm thickness displays an excellent X-ray attenuation efficiency of more than 90% in the photon energy range below 50 keV and 65% at 83 keV, which averagely exceeds ∼3% than that of the 0.25 mm lead plate and ∼5% than that of the 0.65 mm commercial lead apron. Additionally, the coordination between bismuth and leather provides an enhanced tensile and tear strength of ∼10-fold and 3-fold compared with the lead apron. It is worth mentioning that BiINP-LM also displays extra high water-vapor permeability, which is ∼50-fold more than the lead apron. Overall, this work opens up a new prospect for preparing advanced X-ray shielding materials with both excellent X-ray attenuation and outstanding physiomechanical performances.

Structural studies of a manganese(iii) complex with spin-crossover and thermochromic properties

A new Mn^III complex exhibits a gradual spin crossover phenomenon with single crystal thermochromism. A comparative structural study was conducted using octahedral deviation parameters.

Photocrystallographic Studies on Transition Metal Nitrito Metastable Linkage Isomers: Manipulating the Metastable State

The design of solid-state materials whose properties and functions can be manipulated in a controlled manner by the application of light is an important objective in modern materials chemistry. When the material changes property or function, it is helpful if a simple measurable response, such as a change in color, can be detected. Potential applications for such materials are wide ranging, from data storage to smart windows. With the growing emphasis on solid-state materials that have two or more accessible energy states and which exhibit bistability, attention has turned to transition metal complexes that contain ambidentate ligands that can switch between linkage isomeric forms when activated by light. Suitable ligands that show promise in this area include nitrosyls, nitro groups, and coordinated sulfur dioxide molecules, each of which can coordinate to a metal center in more than one bonding mode. A nitrosyl normally coordinates through its N atom (η¹-NO) but when photoactivated can undergo isomerism and coordinate through its O atom (η¹-ON). At a molecular level, converting between these two configurations can act as an “on/off” switch. The analysis of such materials has been aided by the development of photocrystallographic techniques, which allow the full three-dimensional structure of a single crystal of a complex, under photoactivation, to be determined, when it is in either a metastable or short-lived excited state. The technique effectively brings the dimension of “time” to the crystallographic experiment and brings us closer to being able to watch solid-state processes occur in real time.

In this Account, we highlight the advances made in photocrystallography for studying solid-state, photoactivated linkage isomerism and describe the factors that favor the switching process and which allow complete switching between isomers. We demonstrate that control of temperature is key to achieving either a metastable state or an excited state with a specific lifetime. We draw our conclusions from published work on the formation of photoactivated metastable states for nitrosyl and sulfur dioxide complexes and from our own work on photoactivated switching between nitro and nitrito groups. We show that efficient switching between isomers is dependent on the wavelength of light used, on the temperature at which the experiment is carried out, on the flexibility of the crystal lattice, and on both the electronic and steric environment of the ambidentate ligand undergoing isomerism. We have designed and prepared a number of nitro/nitrito isomeric metal complexes that undergo reversible 100% conversion between the two forms at temperatures close to room temperature. Through our fine control over the generation of the metastable states, it should be possible to effectively “dial up” a suitable temperature to give a metastable or an excited state with a desired lifetime.

A structural exploration of anisole accessed through extreme crystallisation conditions

A novel high pressure polymorph of anisole has been discovered and investigated with respect to the known low temperature form.

Energy frameworks and a topological analysis of the supramolecular features in in situ cryocrystallized liquids: tuning the weak interaction landscape via fluorination

Weak intermolecular interactions observed in crystalline materials are often influenced or forced by stronger interactions such as classical hydrogen bonds. Room temperature liquids offer a scenario where such strong interactions are absent so that the role and nature of the weak interactions can be studied more reliably. In this context, we have analyzed the common organic reagent benzoyl chloride (BC) and a series of its fluorinated derivatives using in situ cryocrystallography. The intermolecular interaction energies have been estimated and their topologies explored using energy framework analysis in a series of ten benzoyl chloride analogues, which reveal that the ππ stacking interactions serve as the primary building blocks in these crystal structures. The crystal packing is also stabilized by a variety of interaction motifs involving weak C-HO/F/Cl hydrogen bonds and FF, FCl, and ClCl interactions. It is found that fluorination alters the electrostatic nature of the benzoyl chlorides, with subsequent changes in the formation of different weak interaction motifs. The effects of fluorination on these weak intermolecular interactions have been systematically analyzed further via detailed inputs from a topological analysis of the electron density and Hirshfeld surface analysis.

Magnetically textured powders—an alternative to single-crystal and powder X-ray diffraction methods

Structure determination of materials in their crystalline phase aids in the understanding and design of their functions.

Pharmaceutical cocrystals, salts and polymorphs: Advanced characterization techniques

The main goal of a novel drug development is to obtain it with optimal physiochemical, pharmaceutical and biological properties. Pharmaceutical companies and scientists modify active pharmaceutical ingredients (APIs), which often are cocrystals, salts or carefully selected polymorphs, to improve the properties of a parent drug. To find the best form of a drug, various advanced characterization methods should be used. In this review, we have described such analytical methods, dedicated to solid drug forms. Thus, diffraction, spectroscopic, thermal and also pharmaceutical characterization methods are discussed. They all are necessary to study a solid API in its intrinsic complexity from bulk down to the molecular level, gain information on its structure, properties, purity and possible transformations, and make the characterization efficient, comprehensive and complete. Furthermore, these methods can be used to monitor and investigate physical processes, involved in the drug development, in situ and in real time. The main aim of this paper is to gather information on the current advancements in the analytical methods and highlight their pharmaceutical relevance.

On the use of structured light in nonlinear optics studies of the symmetry group of a crystal

We put forward a technique that allows to extract information about the symmetry group to which certain nonlinear crystals belong using a single illuminating beam. It provides such information by considering the outcome of a nonlinear optics process characterized by the electric nonlinear susceptibility tensor, whose structure is dictated by such symmetry group. As an example, we consider the process of spontaneous parametric down-conversion, when it is pumped with a special type of Bessel beam. The observation of the spatial angular dependence of the lower-frequency generated light provides direct information about the symmetry group of the crystal. We should stress that the choice of the appropriate illumination is of paramount importance for unveiling the sought-after information.

Crystal Structure of a Hidden Protein, YcaC, a Putative Cysteine Hydrolase from Pseudomonas aeruginosa, with and without an Acrylamide Adduct

As part of the ongoing effort to functionally and structurally characterize virulence factors in the opportunistic pathogen Pseudomonas aeruginosa, we determined the crystal structure of YcaC co-purified with the target protein at resolutions of 2.34 and 2.56 Å without a priori knowledge of the protein identity or experimental phases. The three-dimensional structure of YcaC adopts a well-known cysteine hydrolase fold with the putative active site residues conserved. The active site cysteine is covalently bound to propionamide in one crystal form, whereas the second form contains an S-mercaptocysteine. The precise biological function of YcaC is unknown; however, related prokaryotic proteins have functions in antibacterial resistance, siderophore production and NADH biosynthesis. Here, we show that YcaC is exceptionally well conserved across both bacterial and fungal species despite being non-ubiquitous. This suggests that whilst YcaC may not be part of an integral pathway, the function could confer a significant evolutionary advantage to microbial life.

A versatile environmental control cell forin situguest exchange single-crystal diffraction

In situsingle-crystal diffraction experiments provide researchers with the opportunity to study the response of crystalline systems, including metal–organic frameworks and other nanoporous materials, to changing local microenvironments. This paper reports a new environmental control cell that is remarkably easy to use, completely reusable, and capable of delivering static or dynamic vacuum, liquids or gases to a single-crystal sample. Furthermore the device is nearly identical in size to standard single-crystal mounts so a full unrestricted range of motion is expected for most commercial goniometers.In situsingle-crystal X-ray diffraction experiments performed under dynamic gas-flow conditions revealed the cell was capable of stabilizing a novel metastable intermediate in the dehydration reaction of a previously reported metal–organic framework.

Progress and outlook in structural biology of large viral RNAs

The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.

Natural products in medicine: transformational outcome of synthetic chemistry

This review brings to the forefront key synthetic modifications on natural products (NPs) that have yielded successful drugs. The emphasis is placed on the power of targeted chemical transformations in enhancing the therapeutic value of NPs through optimization of pharmacokinetics, stability, potency, and/or selectivity. Multiple classes of NPs such as macrolides, opioids, steroids, and β-lactams used to treat a variety of conditions such as cancers, infections, inflammation are exemplified. Molecular modeling or X-ray structures of NP/protein complexes supporting the observed boost in therapeutic value of the modified NPs are also discussed. Significant advancement in synthetic chemistry, in structure determination, and in the understanding of factors controlling pharmacokinetics can now better position drug discovery teams to undertake NPs as valuable leads. We hope that the beneficial NPs synthetic modifications outlined here will reignite medicinal chemists' interest in NPs and their derivatives.

Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups

Infinite head-to-tail chains of zwitterions present in the crystals of all amino acids are known to be preserved even after structural phase transitions. In order to understand the role of the N-H...O hydrogen bonds linking zwitterions in these chains in structural rearrangements, the crystal structures of the N-methyl derivatives of glycine (N-methylglycine, or sarcosine, with two donors for hydrogen bonding; two polymorphs of N,N-dimethylglycine, DMG-I and DMG-II, with one donor for hydrogen bond; and N,N,N-trimethylglycine, or betaine, with no hydrogen bonds) were studied at different pressures. Methylation has not only excluded the formation of selected hydrogen bonds, but also introduced bulky mobile fragments into the structure. The effects of pressure on the systems of the series were compared with respect to distorting and switching over hydrogen bonds and inducing reorientation of the methylated fragments. Phase transitions with fragmentation of the single crystals into fine powder were observed for partially methylated N-methyl- and N,N-dimethylglycine, whereas the structural changes in betaine were continuous with some peculiar features in the 1.4-2.9 GPa pressure range and accompanied by splitting of the crystals into several large fragments. Structural rearrangements in sarcosine and betaine were strongly dependent on the rate of pressure variation: the higher the rate of increasing pressure, the lower the pressure at which the phase transition occurred.

Femtosecond crystallography with ultrabright electrons and x-rays: capturing chemistry in action

With the recent advances in ultrabright electron and x-ray sources, it is now possible to extend crystallography to the femtosecond time domain to literally light up atomic motions involved in the primary processes governing structural transitions. This review chronicles the development of brighter and brighter electron and x-ray sources that have enabled atomic resolution to structural dynamics for increasingly complex systems. The primary focus is on achieving sufficient brightness using pump-probe protocols to resolve the far-from-equilibrium motions directing chemical processes that in general lead to irreversible changes in samples. Given the central importance of structural transitions to conceptualizing chemistry, this emerging field has the potential to significantly improve our understanding of chemistry and its connection to driving biological processes.