Characterization of Reactive Organometallic Species via MicroED

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction

3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

In crystallo lattice adaptivity triggered by solid-gas reactions of cationic group 7 pincer complexes

The group 7 complexes [M(κ3-2,6-(R2PO)2C5H3N)(CO)2L][BArF4] [M = Mn, R = iPr, L = THF; M = Re, R = tBu, L = vacant site] undergo in crystallo solid-gas reactivity with CO to form the products of THF substitution or CO addition respectively. There is a large, local, adaptive change of [BArF4] anions for M = Mn, whereas for M = Re the changes are smaller and also remote to the site of reactivity.

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet-triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

Electron Diffraction of 3D Molecular Crystals

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

Atomic-Resolution Imaging of Small Organic Molecules on Graphene

Here, we demonstrate atomic-resolution scanning transmission electron microscopy (STEM) imaging of light elements in small organic molecules on graphene. We use low-dose, room-temperature, aberration-corrected STEM to image 2D monolayer and bilayer molecular crystals, followed by advanced image processing methods to create high-quality composite images from ∼10²-10⁴ individual molecules. In metalated porphyrin and phthalocyanine derivatives, these images contain an elementally sensitive contrast with up to 1.3 Å resolution─sufficient to distinguish individual carbon and nitrogen atoms. Importantly, our methods can be applied to molecules with low masses (∼0.6 kDa) and nanocrystalline domains containing just a few hundred molecules, making it possible to study systems for which large crystals cannot easily be grown. Our approach is enabled by low-background graphene substrates, which we show increase the molecules' critical dose by 2-7×. These results indicate a new route for low-dose, atomic-resolution electron microscopy imaging to solve the structures of small organic molecules.

MicroED characterization of a robust cationic σ-alkane complex stabilized by the [B(3,5-(SF5)2C6H3)4]- anion, via on-grid solid/gas single-crystal to single-crystal reactivity

Microcrystalline (∼1 μm) [Rh(Cy₂PCH₂CH₂PCy₂)(norbornadiene)][S-BAr^F₄], [S-BAr^F₄] = [B(3,5-(SF₅)₂C₆H₃)₄]⁻, reacts with H₂ in a single-crystal to single-crystal transformation to form the σ-alkane complex [Rh(Cy₂PCH₂CH₂PCy₂)(norbornane)][S-BAr^F₄], for which the structure was determined by microcrystal Electron Diffraction (microED), to 0.95 Å resolution, via an on-grid hydrogenation, and a complementary single-crystal X-ray diffraction study on larger, but challenging to isolate, crystals. Comparison with the [BAr^F₄]⁻ analogue [Ar^F = 3,5-(CF₃)₂(C₆H₃)] shows that the [S-BAr^F₄]⁻ anion makes the σ-alkane complex robust towards decomposition both thermally and when suspended in pentane. Subsequent reactivity with dissolved ethene in a pentane slurry, forms [Rh(Cy₂PCH₂CH₂PCy₂)(ethene)₂][S-BAr^F₄], and the catalytic dimerisation/isomerisation of ethene to 2-butenes. The increased stability of [S-BAr^F₄]⁻ salts is identified as being due to increased non-covalent interactions in the lattice, resulting in a solid-state molecular organometallic material with desirable stability characteristics.

The thermally and chemically robust σ-alkane complex [Rh(Cy₂PCH₂CH₂PCy₂)(norborane)][B(3,5-(SF₅)₂C₆H₃)₄] is characterized by micro-electron diffraction using on-grid single-crystal to single-crystal reactivity.

Indomethacin Polymorph δ Revealed to be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47-Year-Old Misunderstanding

Indomethacin is a clinically classical non‐steroidal anti‐inflammatory drug that has been marketed since 1965. The third polymorph, Form δ, was discovered by both melt and solution crystallization in 1974. δ‐indomethacin cannot be cultivated as large single crystals suitable for X‐ray crystallography and, therefore, its crystal structure has not yet been determined. Here, we report the structure elucidation of δ‐indomethacin by 3D electron diffraction and reveal the truth that melt‐crystallized and solution‐crystallized δ‐indomethacin are in fact two polymorphs with different crystal structures. We propose to keep the solution‐crystallized polymorph as Form δ and name the melt‐crystallized polymorph as Form θ. Intriguingly, both structures display plastic flexibility based on a slippage mechanism, making indomethacin the first drug to have two plastic polymorphs. This discovery and correction of a 47‐year‐old misunderstanding signify that 3D electron diffraction has become a powerful tool for polymorphic structural studies.

Unraveling the Electrical and Magnetic Properties of Layered Conductive Metal-Organic Framework With Atomic Precision

This paper describes structural elucidation of a layered conductive metal-organic framework (MOF) material Cu₃ (C₆ O₆ )₂ by microcrystal electron diffraction with sub-angstrom precision. This insight enables the first identification of an unusual π-stacking interaction in a layered MOF material characterized by an extremely short (2.73 Å) close packing of the ligand arising from pancake bonding and ordered water clusters within pores. Band structure analysis suggests semiconductive properties of the MOF, which are likely related to the localized nature of pancake bonds and the formation of a singlet dimer of the ligand. The spin of Cu^II within the Kagomé arrangement dominates the paramagnetism of the MOF, leading to strong geometrical magnetic frustration.

A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature

3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).

3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications

In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.

Prospecting for natural products by genome mining and microcrystal electron diffraction

More than 60% of pharmaceuticals are related to natural products (NPs), chemicals produced by living organisms. Despite this, the rate of NP discovery has slowed over the past few decades. In many cases the rate-limiting step in NP discovery is structural characterization. Here we report the use of microcrystal electron diffraction (MicroED), an emerging cryogenic electron microscopy (CryoEM) method, in combination with genome mining to accelerate NP discovery and structural elucidation. As proof of principle we rapidly determine the structure of a new 2-pyridone NP, Py-469, and revise the structure of fischerin, an NP isolated more than 25 years ago, with potent cytotoxicity but hitherto ambiguous structural assignment. This study serves as a powerful demonstration of the synergy of MicroED and synthetic biology in NP discovery, technologies that when taken together will ultimately accelerate the rate at which new drugs are discovered.

CaMn3 IV O4 Cubane Models of the Oxygen-Evolving Complex: Spin Ground States S<9/2 and the Effect of Oxo Protonation

We report the single crystal XRD and MicroED structure, magnetic susceptibility, and EPR data of a series of CaMn₃ ^IV O₄ and YMn₃ ^IV O₄ complexes as structural and spectroscopic models of the cuboidal subunit of the oxygen-evolving complex (OEC). The effect of changes in heterometal identity, cluster geometry, and bridging oxo protonation on the spin-state structure was investigated. In contrast to previous computational models, we show that the spin ground state of CaMn₃ ^IV O₄ complexes and variants with protonated oxo moieties need not be S=9/2. Desymmetrization of the pseudo-C₃ -symmetric Ca(Y)Mn₃ ^IV O₄ core leads to a lower S=5/2 spin ground state. The magnitude of the magnetic exchange coupling is attenuated upon oxo protonation, and an S=3/2 spin ground state is observed in CaMn₃ ^IV O₃ (OH). Our studies complement the observation that the interconversion between the low-spin and high-spin forms of the S₂ state is pH-dependent, suggesting that the (de)protonation of bridging or terminal oxygen atoms in the OEC may be connected to spin-state changes.

An Overview of Microcrystal Electron Diffraction (MicroED)

The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.

Enhanced Gearing Fidelity Achieved Through Macrocyclization of a Solvated Molecular Spur Gear

Molecular spur gear dynamics with high gearing fidelity can be achieved through a careful selection of constituent molecular components that favorably position and maintain the two gears in a meshed configuration. Here, we report the synthesis of a new macrocyclic molecular spur gear with a bibenzimidazole stator combined with a second naphthyl bis-gold-phosphine gold complex stator to place two 3-fold symmetric 9,10-diethynyl triptycene cogs at the optimal distance of 8.1 Å for gearing. Micro electron diffraction (μED) analysis confirmed the formation of the macrocyclic structure and the proper alignment of the triptycene cogs. Gearing dynamics in solution are predicted to be extremely fast and, in fact, were too fast to be observed with variable-temperature ¹H NMR using CD₂Cl₂ as the solvent. A combination of molecular dynamics and metadynamics simulations predict that the barriers for gearing and slippage are ca. 4 kcal mol^-1 and ca. 9 kcal mol^-1, respectively. This system is characterized by enhanced gearing fidelity compared to the acyclic analog. This is achieved by rigidification of the structure, locking the two triptycenes in the preferred gearing distance and orientation.

Microcrystal Electron Diffraction Elucidates Water-Specific Polymorphism-Induced Emission Enhancement of Bis-arylacylhydrazone

Aggregation-induced emission (AIE) phenomena have gained intense interest over the last decades because of its importance in solid-state emission. However, the elucidation of a working mechanism is difficult owing to the limited characterization methods on solid-state molecules, further complicated if dynamic structural changes occur. Here, a series of bis-arylacylhydrazones (BAHs) were synthesized, for which their AIE properties are only turned on by the reversible adsorption of water molecules. We used microcrystal electron diffraction (MicroED) to determine the molecular structures of two BAHs directly from bulk powders (without attempting to grow crystals) prepared in the absence or presence of water adsorption. This study reveals the unambiguous characterization of the dependence of crystal packing on the specific cocrystallization with hydrates. The structural analysis demonstrates that water molecules form strong hydrogen bonds with three neighboring BAH-1, resulting in the almost complete planarization and restriction of the intramolecular rotation of the molecule. MicroED plays an important role in providing a decisive clue for the reversible polymorphism changes induced by the adsorption of water molecules, regulating emissive properties.

Elucidation of Diverse Solid-State Packing in a Family of Electron-Deficient Expanded Helicenes via Microcrystal Electron Diffraction (MicroED)*

Solid-state packing plays a defining role in the properties of a molecular organic material, but it is difficult to elucidate in the absence of single crystals that are suitable for X-ray diffraction. Herein, we demonstrate the coupling of divergent synthesis with microcrystal electron diffraction (MicroED) for rapid assessment of solid-state packing motifs, using a class of chiral nanocarbons-expanded helicenes-as a proof of concept. Two highly selective oxidative dearomatizations of a readily accessible helicene provided a divergent route to four electron-deficient analogues containing quinone or quinoxaline units. Crystallization efforts consistently yielded microcrystals that were unsuitable for single-crystal X-ray diffraction, but ideal for MicroED. This technique facilitated the elucidation of solid-state structures of all five compounds with <1.1 Å resolution. The otherwise-inaccessible data revealed a range of notable packing behaviors, including four different space groups, homochirality in a crystal for a helicene with an extremely low enantiomerization barrier, and nanometer scale cavities.

Ab Initio Determination of Peptide Structures by MicroED

Structural elucidation of small macromolecules such as peptides has recently been facilitated by a growing number of technological advances to existing crystallographic methods. The emergence of electron micro-diffraction (MicroED) of protein nanocrystals under cryogenic conditions has enabled the interrogation of crystalline peptide assemblies only hundreds of nanometers thick. Collection of atomic or near-atomic resolution data by these methods has permitted the ab initio determination of structures of various amyloid-forming peptides, including segments derived from prions and ice-nucleating proteins. This chapter focuses on the process of ab initio structural determination from nano-scale peptide assemblies and other similar molecules.

In Crystallo Snapshots of Rh2-Catalyzed C-H Amination

While X-ray crystallography routinely provides structural characterization of kinetically stable pre-catalysts and intermediates, elucidation of the structures of transient reactive intermediates, which are intimately engaged in bond-breaking and -making during catalysis, is generally not possible. Here, we demonstrate in crystallo synthesis of Rh₂ nitrenoids that participate in catalytic C-H amination, and we characterize these transient intermediates as triplet adducts of Rh₂. Further, we observe the impact of coordinating substrate, which is present in excess during catalysis, on the structure of transient Rh₂ nitrenoids. By providing structural characterization of authentic C-H functionalization intermediates, and not kinetically stabilized model complexes, these experiments provide the opportunity to define critical structure-activity relationships.

Are Organozirconium Reagents Applicable in Current Organic Synthesis?

The search for mild, user-friendly, easily accessible, and robust organometallic reagents is an important feature of organometallic chemistry. Ideally, new methodologies employing organometallics should be developed with respect to practical applications in syntheses of target compounds. In this short review, we investigate if organozirconium reagents can fulfill these criteria. Organozirconium compounds are typically generated via in situ hydrozirconation of alkenes or alkynes with the Schwartz reagent. Alkyl and alkenylzirconium reagents have proven to be convenient in conjugate additions, allylic substitutions, cross-coupling reactions, and additions to carbonyls or imines. Furthermore, the Schwartz reagent itself is a useful reducing agent for polar functional groups.

1 Introduction

2 Synthesis and Generation of the Schwartz Reagent

3 Structure and Properties of Cp2Zr(H)Cl

4 Reactivity of Organozirconium Reagents

4.1 Asymmetric Conjugate Addition

4.2 Asymmetric Allylic Alkylations

4.3 Desymmetrization Reactions

4.4 Cross-Coupling Reactions

4.5 1,2-Additions

5 Conclusions

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.

Experimental Phasing of MicroED Data Using Radiation Damage

We previously demonstrated that microcrystal electron diffraction (MicroED) can be used to determine atomic-resolution structures from vanishingly small three-dimensional crystals. Here, we present an example of an experimentally phased structure using only MicroED data. The structure of a seven-residue peptide is solved starting from differences to the diffraction intensities induced by structural changes due to radiation damage. The same wedge of reciprocal space was recorded twice by continuous-rotation MicroED from a set of 11 individual crystals. The data from the first pass were merged to make a "low-dose dataset." The data from the second pass were similarly merged to form a "damaged dataset." Differences between these two datasets were used to identify a single heavy-atom site from a Patterson difference map, and initial phases were generated. Finally, the structure was completed by iterative cycles of modeling and refinement.

Single crystal growth of water-soluble metal complexes with the help of the nano-crystallization method

Let pipetting robots set up nano crystallization trials of water-soluble metal complexes in order to obtain single crystals!