DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu.

With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.

Tethering Three Radical Cascades for Controlled Termination of Radical Alkyne peri-Annulations: Making Phenalenyl Ketones without Oxidants.

Although Bu3Sn-mediated radical alkyne peri-annulations allow access to phenalenyl ring systems, the oxidative termination of these cascades provides only a limited selection of the possible isomeric phenalenone products with product selectivity controlled by the intrinsic properties of the new cyclic systems. In this work, we report an oxidant-free termination strategy that can overcome this limitation and enable selective access to the full set of isomerically functionalized phenalenones. The key to preferential termination is the preinstallation of a "weak link" that undergoes C-O fragmentation in the final cascade step. Breaking a C-O bond is assisted by entropy, gain of conjugation in the product, and release of stabilized radical fragments. This strategy is expanded to radical exo-dig cyclization cascades of oligoalkynes, which provide access to isomeric π-extended phenalenones. Conveniently, these cascades introduce functionalities (i.e., Bu3Sn and iodide moieties) amenable to further cross-coupling reactions. Consequently, a variety of polyaromatic diones, which could serve as phenalenyl-based open-shell precursors, can be synthesized.

Molecular-level architecture of Chlamydomonas reinhardtii's glycoprotein-rich cell wall.

Microalgae are a renewable and promising biomass for large-scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii. Using in situ solid-state and sensitivity-enhanced nuclear magnetic resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower-molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.

Role of Protons in and around Strongly Coupled Nitroxide Biradicals for Cross-Effect Dynamic Nuclear Polarization.

In magic angle spinning dynamic nuclear polarization (DNP), biradicals such as bis-nitroxides are used to hyperpolarize protons under microwave irradiation through the cross-effect mechanism. This mechanism relies on electron-electron spin interactions (dipolar coupling and exchange interaction) and electron-nuclear spin interactions (hyperfine coupling) to hyperpolarize the protons surrounding the biradical. This hyperpolarization is then transferred to the bulk sample via nuclear spin diffusion. However, the involvement of the protons in the biradical in the cross-effect DNP process has been under debate. In this work, we address this question by exploring the hyperpolarization pathways in and around bis-nitroxides. We demonstrate that for biradicals with strong electron-electron interactions, as in the case of the AsymPols, the protons on the biradical may not be necessary to quickly generate hyperpolarization. Instead, such biradicals can efficiently, and directly, polarize the surrounding protons of the solvent. The findings should impact the design of the next generation of biradicals.

AsymPol-TEKs as efficient polarizing agents for MAS-DNP in glass matrices of non-aqueous solvents.

Two polarizing agents from the AsymPol family, AsymPol-TEK and cAsymPol-TEK (methyl-free version) are introduced for MAS-DNP applications in non-aqueous solvents. The performance of these new biradicals is rationalized in detail using a combination of electron paramagnetic resonance spectroscopy, density functional theory, molecular dynamics and quantitative MAS-DNP spin dynamics simulations. By slightly modifying the experimental protocol to keep the sample temperature low at insertion, we are able to obtain reproducable DNP-NMR data with 1,1,2,2-tetrachloroethane (TCE) at 100 K, which facilitates optimization and comparison of different polarizing agents. At intermediate magnetic fields, AsymPol-TEK and cAsymPol-TEK provide 1.5 to 3-fold improvement in sensitivity compared to TEKPol, one of the most widely used polarizing agents for organic solvents, with significantly shorter DNP build-up times of ∼1 s and ∼2 s at 9.4 and 14.1 T respectively. In the course of the work, we also isolated and characterized two diastereoisomers that can form during the synthesis of AsymPol-TEK; their difference in performance is described and discussed. Finally, the advantages of the AsymPol-TEKs are demonstrated by recording 2D 13C-13C correlation experiments at natural 13C-abundance of proton-dense microcrystals and by polarizing the surface of ZnO nanocrystals (NCs) coated with diphenyl phosphate ligands. For those experiments, cAsymPol-TEK yielded a three-fold increase in sensitivity compared to TEKPol, corresponding to a nine-fold time saving.

Heterotypic Interactions between the 40- and 42-Residue Isoforms of ß-Amyloid Peptides on Lipid Bilayer Surfaces.

Co-aggregation involving different amyloidogenic sequences has been emphasized recently in the modified amyloid cascade hypothesis. Yet, molecular-level interactions between two predominant ß-amyloid peptide sequences, Aß40 and Aß42, in the fibrillation process in membrane-mimicked environments remain unclear. Here, we report biophysical evidence that demonstrates the molecular-level interactions between Aß40 and Aß42 at the membrane-associated conucleation stage using dynamic nuclear polarization-enhanced solid-state NMR spectroscopy. These residue-specific contacts are distinguished from those reported in mature fibrils formed by either Aß40 or Aß42. Meanwhile, site-specific interactions between Aß and lipid molecules and modulation of microsecond-time-scale lipid dynamics are observed, which may be responsible for the more rapid and significant membrane content leakage compared to that with Aß40 alone.

Peculiar Phosphonate Modifications of Velvet Worm Slime Revealed by Advanced Nuclear Magnetic Resonance and Mass Spectrometry.

Nature is rich with examples of highly specialized biological materials produced by organisms for functions, including defense, hunting, and protection. Along these lines, velvet worms (Onychophora) expel a protein-based slime used for hunting and defense that upon shearing and dehydration forms fibers as stiff as thermoplastics. These fibers can dissolve back into their precursor proteins in water, after which they can be drawn into new fibers, providing biological inspiration to design recyclable materials. Elevated phosphorus content in velvet worm slime was previously observed and putatively ascribed to protein phosphorylation. Here, we show instead that phosphorus is primarily present as phosphonate moieties in the slime of distantly related velvet worm species. Using high-resolution nuclear magnetic resonance (NMR), natural abundance dynamic nuclear polarization (DNP), and mass spectrometry (MS), we demonstrate that 2-aminoethyl phosphonate (2-AEP) is associated with glycans linked to large slime proteins, while transcriptomic analyses confirm the expression of 2-AEP synthesizing enzymes in slime glands. The evolutionary conservation of this rare protein modification suggests an essential functional role of phosphonates in velvet worm slime and should stimulate further study of the function of this unusual chemical modification in nature.

Terahertz EPR spectroscopy using a 36-tesla high-homogeneity series-connected hybrid magnet.

Electron Paramagnetic Resonance (EPR) is a powerful technique to study materials and biological samples on an atomic scale. High-field EPR in particular enables extracting very small g-anisotropies in organic radicals and half-filled 3d and 4f metal ions such as MnII (3d5) or GdIII (4f7), and resolving EPR signals from unpaired spins with very close g-values, both of which provide high-resolution details of the local atomic environment. Before the recent commissioning of the high-homogeneity Series Connected Hybrid magnet (SCH, superconducting + resistive) at the National High Magnetic Field Laboratory (NHMFL), the highest-field, high-resolution EPR spectrometer available was limited to 25 T using a purely resistive "Keck" magnet at the NHMFL. Herein, we report the first EPR experiments performed using the SCH magnet capable of reaching the field of 36 T, corresponding to an EPR frequency of 1 THz for g = 2. The magnet's intrinsic homogeneity (25 ppm, that is 0.9 mT at 36 T over 1 cm diameter, 1 cm length cylinder) was previously established by NMR. We characterized the magnet's temporal stability (5 ppm, which is 0.2 mT at 36 T over one-minute, the typical acquisition time) using 2,2-diphenyl-1-picrylhydrazyl (DPPH). This high resolution enables resolving the weak g-anisotropy of 1,3-bis(diphenylene)-2-phenylallyl (BDPA), Δg = 2.5 × 10-4 obtained from measurements at 932 GHz and 33 T. Subsequently, we recorded EPR spectra at multiple frequencies for two GdIII complexes with potential applications as spin labels. We demonstrated a significant reduction in line broadening in Gd[DTPA], attributed to second order zero field splitting, and a resolution enhancement of g-tensor anisotropy for Gd[sTPATCN]-SL.

PyrroTriPol: a semi-rigid trityl-nitroxide for high field dynamic nuclear polarization.

Magic angle spinning (MAS) dynamic nuclear polarization (DNP) has significantly broadened the scope of solid-state NMR to study biomolecular systems and materials. In recent years, the advent of very high field DNP combined with fast MAS has brought new challenges in the design of polarizing agents (PA) used to enhance nuclear spin polarization. Here, we present a trityl-nitroxide PA family based on a piperazine linker, named PyrroTriPol, for both aqueous and organic solutions. These new radicals have similar properties to that of TEMTriPol-I and can be readily synthesized, and purified in large quantities thereby ensuring widespread application. The family relies on a rigid bridge connecting the trityl and the nitroxide offering a better control of the electron spin-spin interactions thus providing improved performance across a broad range of magnetic fields and MAS frequencies while requiring reduced microwave power compared to bis-nitroxides. We demonstrate the efficiency of the PyrroTriPol family under a magnetic field of 9.4, 14.1 and 18.8 T with respect to TEMTriPol-I. In particular, the superiority of PyrroTriPol was demonstrated on γ-Al2O3 nanoparticles which enabled the acquisition of a high signal-to-noise surface-selective 27Al multiple-quantum MAS experiment at 18.8 T and 40 kHz MAS frequency.

17O solid state NMR as a valuable tool for deciphering reaction mechanisms in mechanochemistry: the case study on the 17O-enrichment of hydrated Ca-pyrophosphate biominerals.

The possibility of enriching in 17O the water molecules within hydrated biominerals belonging to the Ca-pyrophosphate family was investigated, using liquid assisted grinding (LAG) in the presence of 17O-labelled water. Two phases with different hydration levels, namely triclinic calcium pyrophosphate dihydrate (Ca2P2O7·2H2O, denoted t-CPPD) and monoclinic calcium pyrophosphate tetrahydrate (Ca2P2O7·4H2O, denoted m-CPPT ß) were enriched in 17O using a "post-enrichment" strategy, in which the non-labelled precursors were ground under gentle milling conditions in the presence of stoichiometric quantities of 17O-enriched water (introduced here in very small volumes ∼10 µL). Using high-resolution 17O solid-state NMR (ssNMR) analyses at multiple magnetic fields, and dynamic nuclear polarisation (DNP)-enhanced 17O NMR, it was possible to show that the labelled water molecules are mainly located at the core of the crystal structures, but that they can enter the lattice in different ways, namely by dissolution/recrystallisation or by diffusion. Overall, this work sheds light on the importance of high-resolution 17O NMR to help decipher the different roles that water can play as a liquid-assisted grinding agent and as a reagent for 17O-isotopic enrichment.

Design and Synthesis of Kekulè and Non-Kekulè Diradicaloids via the Radical Periannulation Strategy: The Power of Seven Clar's Sextets.

This work introduces an approach to uncoupling electrons via maximum utilization of localized aromatic units, i.e., the Clar's π-sextets. To illustrate the utility of this concept to the design of Kekulé diradicaloids, we have synthesized a tridecacyclic polyaromatic system where a gain of five Clar's sextets in the open-shell form overcomes electron pairing and leads to the emergence of a high degree of diradical character. According to unrestricted symmetry-broken UCAM-B3LYP calculations, the singlet diradical character in this core system is characterized by the y0 value of 0.98 (y0 = 0 for a closed-shell molecule, y0 = 1 for pure diradical). The efficiency of the new design strategy was evaluated by comparing the Kekulé system with an isomeric non-Kekulé diradical of identical size, i.e., a system where the radical centers cannot couple via resonance. The calculated singlet-triplet gap, i.e., the ΔEST values, in both of these systems approaches zero: -0.3 kcal/mol for the Kekulé and +0.2 kcal/mol for the non-Kekulé diradicaloids. The target isomeric Kekulé and non-Kekulé systems were assembled using a sequence of radical periannulations, cross-coupling, and C-H activation. The diradicals are kinetically stabilized by six tert-butyl substituents and (triisopropylsilyl)acetylene groups. Both molecules are NMR-inactive but electron paramagnetic resonance (EPR)-active at room temperature. Cyclic voltammetry revealed quasi-reversible oxidation and reduction processes, consistent with the presence of two nearly degenerate partially occupied molecular orbitals. The experimentally measured ΔEST value of -0.14 kcal/mol confirms that K is, indeed, a nearly perfect singlet diradical.

MAS-DNP enables NMR studies of insect wings.

NMR is a valuable tool for studying insects. Solid-state NMR has been used to obtain the chemical composition and gain insight into the sclerotization process of exoskeletons. There is typically little difficulty in obtaining sufficient sample quantity for exoskeletons. However, obtaining enough sample of other insect components for solid-state NMR experiments can be problematic while isotopically enriching them is near impossible. This is especially the case for insect wing membranes which is of interest to us. Issues with obtaining sufficient sample are the thickness of wing membranes is on the order of microns, each membrane region is surrounded by veins and occupies a small area, and the membranes are separated from the wing by physical dissection. Accordingly, NMR signal enhancement methods are needed. MAS-DNP has a track record of providing significant signal enhancements for a wide variety of materials. Here we demonstrate that MAS-DNP is useful for providing high quality one-dimensional and two-dimensional solid-state NMR spectra on cicada wing membrane at natural isotopic abundance.

Current limitations of solid-state NMR in carbohydrate and cell wall research.

High-resolution investigation of cell wall materials has emerged as an important application of biomolecular solid-state NMR (ssNMR). Multidimensional correlation experiments have become a standard method for obtaining sufficient spectral resolution to determine the polymorphic structure of carbohydrates and address biochemical questions regarding the supramolecular organization of cell walls. Using plant cellulose and matrix polysaccharides as examples, we will review how the multifaceted complexity of polysaccharide structure is impeding the resonance assignment process and assess the available biochemical and spectroscopic approaches that could circumvent this barrier. We will emphasize the ineffectiveness of the current methods in reconciling the ever-growing dataset and deriving structural information. We will evaluate the protocols for achieving efficient and homogeneous hyperpolarization across the cell wall material using magic-angle spinning dynamic nuclear polarization (MAS-DNP). Critical questions regarding the line-broadening effects of cell wall molecules at cryogenic temperature and by paramagnetic biradicals will be considered. Finally, the MAS-DNP method will be placed into a broader context with other structural characterization techniques, such as cryo-electron microscopy, to advance ssNMR research in carbohydrate and cell wall biomaterials.

Solid-state NMR analysis of unlabeled fungal cell walls from Aspergillus and Candida species.

Fungal infections cause high mortality in immunocompromised individuals, which has emerged as a significant threat to human health. The efforts devoted to the development of antifungal agents targeting the cell wall polysaccharides have been hindered by our incomplete picture of the assembly and remodeling of fungal cell walls. High-resolution solid-state nuclear magnetic resonance (ss NMR) studies have substantially revised our understanding of the polymorphic structure of polysaccharides and the nanoscale organization of cell walls in Aspergillus fumigatus and multiple other fungi. However, this approach requires 13C/15N-enrichment of the sample being studied, severely restricting its application. Here we employ the dynamic nuclear polarization (DNP) technique to compare the unlabeled cell wall materials of A. fumigatus and C. albicans prepared using both liquid and solid media. For each fungus, we have identified a highly conserved carbohydrate core for the cell walls of conidia and mycelia, and from liquid and solid cultures. Using samples prepared in different media, the recently identified function of α-glucan, which packs with chitin to form the mechanical centers, has been confirmed through conventional ss NMR measurements of polymer dynamics. These timely efforts not only validate the structural principles recently discovered for A. fumigatus cell walls in different morphological stages, but also open up the possibility of extending the current investigation to other fungal materials and cellular systems that are challenging to label.

Spinning-Driven Dynamic Nuclear Polarization with Optical Pumping.

We propose a new, more efficient, and potentially cost effective, solid-state nuclear spin hyperpolarization method combining the cross-effect mechanism and electron spin optical hyperpolarization in rotating solids. We first demonstrate optical hyperpolarization in the solid state at low temperatures and low field and then investigate its field dependence to obtain the optimal condition for high-field electron spin hyperpolarization. The results are then incorporated into advanced magic-angle spinning dynamic nuclear polarization (MAS-DNP) numerical simulations that show that optically pumped MAS-DNP could yield breakthrough enhancements at very high magnetic fields. Based on these investigations, enhancements greater than the ratio of electron to nucleus magnetic moments (>658 for 1H) are possible without microwave irradiation. This could solve at once the MAS-DNP performance decrease with increasing field and the high cost of MAS-DNP instruments at very high fields.

Structure of In Vitro-Synthesized Cellulose Fibrils Viewed by Cryo-Electron Tomography and 13C Natural-Abundance Dynamic Nuclear Polarization Solid-State NMR.

Cellulose, the most abundant biopolymer, is a central source for renewable energy and functionalized materials. In vitro synthesis of cellulose microfibrils (CMFs) has become possible using purified cellulose synthase (CESA) isoforms from Physcomitrium patens and hybrid aspen. The exact nature of these in vitro fibrils remains unknown. Here, we characterize in vitro-synthesized fibers made by CESAs present in membrane fractions of P. patens over-expressing CESA5 by cryo-electron tomography and dynamic nuclear polarization (DNP) solid-state NMR. DNP enabled measuring two-dimensional 13C-13C correlation spectra without isotope-labeling of the fibers. Results show structural similarity between in vitro fibrils and native CMF in plant cell walls. Intensity quantifications agree with the 18-chain structural model for plant CMF and indicate limited fibrillar bundling. The in vitro system thus reveals insights into cell wall synthesis and may contribute to novel cellulosic materials. The integrated DNP and cryo-electron tomography methods are also applicable to structural studies of other carbohydrate-based biomaterials.

Highly Efficient Polarizing Agents for MAS-DNP of Proton-Dense Molecular Solids.

Efficiently hyperpolarizing proton-dense molecular solids through dynamic nuclear polarization (DNP) solid-state NMR is still an unmet challenge. Polarizing agents (PAs) developed so far do not perform well on proton-rich systems, such as organic microcrystals and biomolecular assemblies. Herein we introduce a new PA, cAsymPol-POK, and report outstanding hyperpolarization efficiency on 12.76 kDa U-13 C,15 N-labeled LecA protein and pharmaceutical drugs at high magnetic fields (up to 18.8 T) and fast magic angle spinning (MAS) frequencies (up to 40 kHz). The performance of cAsymPol-POK is rationalized by MAS-DNP simulations combined with electron paramagnetic resonance (EPR), density functional theory (DFT) and molecular dynamics (MD). This work shows that this new biradical is compatible with challenging biomolecular applications and unlocks the rapid acquisition of 13 C-13 C and 15 N-13 C correlations of pharmaceutical drugs at natural isotopic abundance, which are key experiments for structure determination.

Dynamic nuclear polarization-enhanced, double-quantum filtered 13C-13C dipolar correlation spectroscopy of natural 13C abundant bone-tissue biomaterial.

Here, we describe a method for obtaining a dynamic nuclear polarization (DNP)-enhanced double-quantum filtered (DQF) two-dimensional (2D) dipolar 13C-13C correlation spectra of bone-tissue material at natural 13C abundance. DNP-enhanced DQF 2D dipolar 13C-13C spectra were obtained using a few different mixing times of the dipolar-assisted rotational resonance (DARR) scheme and these spectra were compared to a conventional 2D through-space double-quantum (DQ)-single-quantum (SQ) correlation spectrum. While this scheme can only be used for an assignment purpose to reveal the carbon-carbon connectivity within a residue, the DQF 13C-13C dipolar correlation scheme introduced here can be used to obtain longer distance carbon-carbon constraints. A DQF pulse block is placed before the DARR mixing scheme for removing dominant 13C single-quantum (SQ) signals because these SQ 13C signals are overwhelmingly large compared to those 13C-13C dipolar cross-peaks generated and therefore saturate the dynamic range of the NMR detection. This approach exhibits strong enough 2D cross-peaks in a dipolar 13C-13C correlation spectrum and potentially provides pairwise 13C-13C dipolar constraints because the dipolar truncation effect as well as multi-step signal propagations involving a spin cluster that contains more than two spins can be ignored probabilistically. To obtain fast signal averaging, AsymPolPOK was used to provide a short 1H DNP signal build-up time (1.3 s) and to expedite our MAS DNP NMR acquisitions while still maintaining a satisfactory DNP enhancement factor (ε = 50). Under long DARR mixing, a t1-noise-like artifact was observed at a site that possesses a large chemical shift anisotropy (CSA) and a few different strategies to address this problem were discussed.

Carbohydrate-aromatic interface and molecular architecture of lignocellulose.

Plant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways.

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate.

NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze ß-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate ß-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue ßLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cß and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.