Structure Determination of Biogenic Crystals Directly from 3D Electron Diffraction Data.

Highly reflective assemblies of purine, pteridine, and flavin crystals are used in the coloration and visual systems of many different animals. However, structure determination of biogenic crystals by single-crystal XRD is challenging due to the submicrometer size and beam sensitivity of the crystals, and powder XRD is inhibited due to the small volumes of powders, crystalline impurity phases, and significant preferred orientation. Consequently, the crystal structures of many biogenic materials remain unknown. Herein, we demonstrate that the 3D electron diffraction (3D ED) technique provides a powerful alternative approach, reporting the successful structure determination of biogenic guanine crystals (from spider integument, fish scales, and scallop eyes) from 3D ED data confirmed by analysis of powder XRD data. The results show that all biogenic guanine crystals studied are the previously known ß-polymorph. This study highlights the considerable potential of 3D ED for elucidating the structures of biogenic molecular crystals in the nanometer-to-micrometer size range. This opens up an important opportunity in the development of organic biomineralization, for which structural knowledge is critical for understanding the optical functions of biogenic materials and their possible applications as sustainable, biocompatible optical materials.

Exploiting solid-state dynamic nuclear polarization NMR spectroscopy to establish the spatial distribution of polymorphic phases in a solid material.

Solid-state DNP NMR can enhance the ability to detect minor amounts of solid phases within heterogenous materials. Here we demonstrate that NMR contrast based on the transport of DNP-enhanced polarization can be exploited in the challenging case of early detection of a small amount of a minor polymorphic phase within a major polymorph, and we show that this approach can yield quantitative information on the spatial distribution of the two polymorphs. We focus on the detection of a minor amount (<4%) of polymorph III of m-aminobenzoic acid within a powder sample of polymorph I at natural isotopic abundance. Based on proposed models of the spatial distribution of the two polymorphs, simulations of 1H spin diffusion allow NMR data to be calculated for each model as a function of particle size and the relative amounts of the polymorphs. A comparison between simulated and experimental NMR data allows the model(s) best representing the spatial distribution of the polymorphs in the system to be established.

Unraveling the Complex Solid-State Phase Transition Behavior of 1-Iodoadamantane, a Material for Which Ostensibly Identical Crystals Undergo Different Transformation Pathways.

Phase transitions in crystalline molecular solids have important implications in the fundamental understanding of materials properties and in the development of materials applications. Herein, we report the solid-state phase transition behavior of 1-iodoadamantane (1-IA) investigated using a multi-technique strategy [synchrotron powder X-ray diffraction (XRD), single-crystal XRD, solid-state NMR, and differential scanning calorimetry (DSC)], which reveals complex phase transition behavior on cooling from ambient temperature to ca. 123 K and on subsequent heating to the melting temperature (348 K). Starting from the known phase of 1-IA at ambient temperature (phase A), three low-temperature phases are identified (phases B, C, and D); the crystal structures of phases B and C are reported, together with a re-determination of the structure of phase A. Remarkably, single-crystal XRD shows that some individual crystals of phase A transform to phase B, while other crystals of phase A transform instead to phase C. Results (from powder XRD and DSC) on cooling a powder sample of phase A are fully consistent with this behavior while also revealing an additional transformation pathway from phase A to phase D. Thus, on cooling, a powder sample of phase A transforms partially to phase C (at 229 K), partially to phase D (at 226 K) and partially to phase B (at 211 K). During the cooling process, each of the phases B, C, and D is formed directly from phase A, and no transformations are observed between phases B, C, and D. On heating the resulting triphasic powder sample of phases B, C, and D from 123 K, phase B transforms to phase D (at 211 K), followed by the transformation of phase D to phase C (at 255 K), and finally, phase C transforms to phase A (at 284 K). From these observations, it is apparent that different crystals of phase A, which are ostensibly identical at the level of information revealed by XRD, must actually differ in other aspects that significantly influence their low-temperature phase transition pathways. This unusual behavior will stimulate future studies to gain deeper insights into the specific properties that control the phase transition pathways in individual crystals of this material.

Boron Nitride-Doped Polyphenylenic Organogels.

Herein, we describe the synthesis of the first boron nitride-doped polyphenylenic material obtained through a [4 + 2] cycloaddition reaction between a triethynyl borazine unit and a biscyclopentadienone derivative, which undergoes organogel formation in chlorinated solvents (the critical jellification concentration is 4% w/w in CHCl3). The polymer has been characterized extensively by Fourier-transform infrared spectroscopy, solid-state 13C NMR, solid-state 11B NMR, and by comparison with the isolated monomeric unit. Furthermore, the polymer gels formed in chlorinated solvents have been thoroughly characterized and studied, showing rheological properties comparable to those of polyacrylamide gels with a low crosslinker percentage. Given the thermal and chemical stability, the material was studied as a potential support for solid-state electrolytes. showing properties comparable to those of polyethylene glycol-based electrolytes, thus presenting great potential for the application of this new class of material in lithium-ion batteries.

A structure determination protocol based on combined analysis of 3D-ED data, powder XRD data, solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine.

We report the crystal structure of a new polymorph of l-tyrosine (denoted the ß polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic 13C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state 13C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the ß polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and ß polymorphs.

Biogenic Guanine Crystals Are Solid Solutions of Guanine and Other Purine Metabolites.

Highly reflective crystals of the nucleotide base guanine are widely distributed in animal coloration and visual systems. Organisms precisely control the morphology and organization of the crystals to optimize different optical effects, but little is known about how this is achieved. Here we examine a fundamental question that has remained unanswered after over 100 years of research on guanine: what are the crystals made of? Using solution-state and solid-state chemical techniques coupled with structural analysis by powder XRD and solid-state NMR, we compare the purine compositions and the structures of seven biogenic guanine crystals with different crystal morphologies, testing the hypothesis that intracrystalline dopants influence the crystal shape. We find that biogenic "guanine" crystals are not pure crystals but molecular alloys (aka solid solutions and mixed crystals) of guanine, hypoxanthine, and sometimes xanthine. Guanine host crystals occlude homogeneous mixtures of other purines, sometimes in remarkably large amounts (up to 20% of hypoxanthine), without significantly altering the crystal structure of the guanine host. We find no correlation between the biogenic crystal morphology and dopant content and conclude that dopants do not dictate the crystal morphology of the guanine host. The ability of guanine crystals to host other molecules enables animals to build physiologically "cheaper" crystals from mixtures of metabolically available purines, without impeding optical functionality. The exceptional levels of doping in biogenic guanine offer inspiration for the design of mixed molecular crystals that incorporate multiple functionalities in a single material.

Solid-State Structural Properties of Alloxazine Determined from Powder XRD Data in Conjunction with DFT-D Calculations and Solid-State NMR Spectroscopy: Unraveling the Tautomeric Identity and Pathways for Tautomeric Interconversion.

We report the solid-state structural properties of alloxazine, a tricyclic ring system found in many biologically important molecules, with structure determination carried out directly from powder X-ray diffraction (XRD) data. As the crystal structures containing the alloxazine and isoalloxazine tautomers both give a high-quality fit to the powder XRD data in Rietveld refinement, other techniques are required to establish the tautomeric form in the solid state. In particular, high-resolution solid-state 15N NMR data support the presence of the alloxazine tautomer, based on comparison between isotropic chemical shifts in the experimental 15N NMR spectrum and the corresponding values calculated for the crystal structures containing the alloxazine and isoalloxazine tautomers. Furthermore, periodic DFT-D calculations at the PBE0-MBD level indicate that the crystal structure containing the alloxazine tautomer has significantly lower energy. We also report computational investigations of the interconversion between the tautomeric forms in the crystal structure via proton transfer along two intermolecular N-H···N hydrogen bonds; DFT-D calculations at the PBE0-MBD level indicate that the tautomeric interconversion is associated with a lower energy transition state for a mechanism involving concerted (rather than sequential) proton transfer along the two hydrogen bonds. However, based on the relative energies of the crystal structures containing the alloxazine and isoalloxazine tautomers, it is estimated that under conditions of thermal equilibrium at ambient temperature, more than 99.9% of the molecules in the crystal structure will exist as the alloxazine tautomer.

Orbital Mapping of Semiconducting Perylenes on Cu(111).

Semiconducting O-doped polycyclic aromatic hydrocarbons constitute a class of molecules whose optoelectronic properties can be tailored by acting on the π-extension of the carbon-based frameworks and on the oxygen linkages. Although much is known about their photophysical and electrochemical properties in solution, their self-assembly interfacial behavior on solid substrates has remained unexplored so far. In this paper, we have focused our attention on the on-surface self-assembly of O-doped bi-perylene derivatives. Their ability to assemble in ordered networks on Cu(111) single-crystalline surfaces allowed a combination of structural, morphological, and spectroscopic studies. In particular, the exploitation of the orbital mapping methodology based on angle-resolved photoemission spectroscopy, with the support of scanning tunneling microscopy and low-energy electron diffraction, allowed the identification of both the electronic structure of the adsorbates and their geometric arrangement. Our multi-technique experimental investigation includes the structure determination from powder X-ray diffraction data for a specific compound and demonstrates that the electronic structure of such large molecular self-assembled networks can be studied using the reconstruction methods of molecular orbitals from photoemission data even in the presence of segregated chiral domains.

Monitoring Crystallization Processes in Confined Porous Materials by Dynamic Nuclear Polarization Solid-State Nuclear Magnetic Resonance.

Establishing mechanistic understanding of crystallization processes at the molecular level is challenging, as it requires both the detection of transient solid phases and monitoring the evolution of both liquid and solid phases as a function of time. Here, we demonstrate the application of dynamic nuclear polarization (DNP) enhanced NMR spectroscopy to study crystallization under nanoscopic confinement, revealing a viable approach to interrogate different stages of crystallization processes. We focus on crystallization of glycine within the nanometric pores (7-8 nm) of a tailored mesoporous SBA-15 silica material with wall-embedded TEMPO radicals. The results show that the early stages of crystallization, characterized by the transition from the solution phase to the first crystalline phase, are straightforwardly observed using this experimental strategy. Importantly, the NMR sensitivity enhancement provided by DNP allows the detection of intermediate phases that would not be observable using standard solid-state NMR experiments. Our results also show that the metastable ß polymorph of glycine, which has only transient existence under bulk crystallization conditions, remains trapped within the pores of the mesoporous SBA-15 silica material for more than 200 days.

Direct-Space Structure Determination of Covalent Organic Frameworks from 3D Electron Diffraction Data.

Structure determination of covalent organic frameworks (COFs) with atomic precision is a bottleneck that hinders the development of COF chemistry. Although three-dimensional electron diffraction (3D-ED) data has been used to solve structures of sub-micrometer-sized COFs, successful structure solution is not guaranteed as the data resolution is usually low. We demonstrate that the direct-space strategy for structure solution, implemented using a genetic algorithm (GA), is a successful approach for structure determination of COF-300 from 3D-ED data. Structural models with different geometric constraints were considered in the GA calculations, with successful structure solution achieved from room-temperature 3D-ED data with a resolution as low as ca. 3.78 Å. The generality of this strategy was further verified for different phases of COF-300. This study demonstrates a viable strategy for structure solution of COF materials from 3D-ED data of limited resolution, which may facilitate the discovery of new COF materials in the future.

Boron-Nitrogen-Doped Nanographenes: A Synthetic Tale from Borazine Precursors.

In this work, a comprehensive account of the authors' synthetic efforts to prepare borazino-doped hexabenzocoronenes by using the Friedel-Crafts-type electrophilic aromatic substitution is reported. Hexafluoro-functionalized aryl borazines, bearing an ortho fluoride leaving group on each of the N- and B-aryl rings, was shown to lead to cascade-type electrophilic aromatic substitution events in the stepwise C-C bond formation, giving higher yields of borazinocoronenes than those obtained with borazine precursors bearing fluoride leaving groups at the ortho positions of the B-aryl substituents. By using this pathway, an unprecedented boroxadizine-doped PAH featuring a gulf-type periphery could be isolated, and its structure proven by single-crystal X-ray diffraction analysis. Mechanistic studies on the stepwise Friedel-Crafts-type cyclization suggest that the mechanism of the planarization reaction proceeds through extension of the π system. To appraise the doping effect of the boroxadizine unit on the optoelectronic properties of topology-equivalent molecular graphenes, the all-carbon and pyrylium PAH analogues, all featuring a gulf-type periphery, were also prepared. As already shown for the borazino-doped hexabenzocoronene, the replacement of the central benzene ring by its B3 N2 O congener widens the HOMO-LUMO gap and dramatically enhances the fluorescence quantum yield.

Manometric real-time studies of the mechanochemical synthesis of zeolitic imidazolate frameworks.

We demonstrate a simple method for real-time monitoring of mechanochemical synthesis of metal-organic frameworks, by measuring changes in pressure of gas produced in the reaction. Using this manometric method to monitor the mechanosynthesis of the zeolitic imidazolate framework ZIF-8 from basic zinc carbonate reveals an intriguing feedback mechanism in which the initially formed ZIF-8 reacts with the CO2 byproduct to produce a complex metal carbonate phase, the structure of which is determined directly from powder X-ray diffraction data. We also show that the formation of the carbonate phase may be prevented by addition of excess ligand. The excess ligand can subsequently be removed by sublimation, and reused. This enables not only the synthesis but also the purification, as well as the activation of the MOF to be performed entirely without solvent.

Exploiting in situ NMR to monitor the formation of a metal-organic framework.

The formation processes of metal-organic frameworks are becoming more widely researched using in situ techniques, although there remains a scarcity of NMR studies in this field. In this work, the synthesis of framework MFM-500(Ni) has been investigated using an in situ NMR strategy that provides information on the time-evolution of the reaction and crystallization process. In our in situ NMR study of MFM-500(Ni) formation, liquid-phase 1H NMR data recorded as a function of time at fixed temperatures (between 60 and 100 °C) afford qualitative information on the solution-phase processes and quantitative information on the kinetics of crystallization, allowing the activation energies for nucleation (61.4 ± 9.7 kJ mol-1) and growth (72.9 ± 8.6 kJ mol-1) to be determined. Ex situ small-angle X-ray scattering studies (at 80 °C) provide complementary nanoscale information on the rapid self-assembly prior to MOF crystallization and in situ powder X-ray diffraction confirms that the only crystalline phase present during the reaction (at 90 °C) is phase-pure MFM-500(Ni). This work demonstrates that in situ NMR experiments can shed new light on MOF synthesis, opening up the technique to provide better understanding of how MOFs are formed.

Rationalization of the X-ray photoelectron spectroscopy of aluminium phosphates synthesized from different precursors.

The aim of this paper is to clarify the assignments of X-ray photoelectron spectra of aluminium phosphate materials prepared from the reaction of phosphoric acid with three different aluminium precursors [Al(OH)3, Al(NO3)3 and AlCl3] at different annealing temperatures. The materials prepared have been studied by X-ray photoelectron spectroscopy (XPS), powder X-ray diffraction (XRD), infrared spectroscopy and high-resolution solid-state 31P NMR spectroscopy. A progressive polymerization from orthophosphate to metaphosphates is observed by XRD, ATR-FTIR and solid state 31P NMR, and on this basis the oxygen states observed in the XP spectra at 532.3 eV and 533.7 eV are assigned to P-O-Al and P-O-P environments, respectively. The presence of cyclic polyphosphates at the surface of the samples is also evident.

Reply to comment on Couzi et al. (2018): a phenomenological model for structural phase transitions in incommensurate alkane/urea inclusion compounds.

In a recent paper (Couzi et al. 2018 R. Soc. open sci. 5, 180058. (doi:10.1098/rsos.180058)), we proposed a new phenomenological model to account for the I↔II↔"III" phase sequence in incommensurate n-alkane/urea inclusion compounds, which represents an alternative interpretation to that proposed in work of Toudic et al. In a Comment (Toudic et al. 2019 R. Soc. open sci. 6, 182073. (doi:10.1098/rsos.182073)), Toudic et al. have questioned our assignment of the superspace group of phase II of n-nonadecane/urea, which they have previously assigned, based on a (3 + 2)-dimensional superspace, as C2221(00γ)(10δ). In this Reply, we present new results from a comprehensive synchrotron single-crystal X-ray diffraction study of n-nonadecane/urea, involving measurements as a detailed function of temperature across the I↔II↔"III" phase transition sequence. Our results demonstrate conclusively that "main reflections" (h, k, l, 0) with h+k odd are observed in phase II of n-nonadecane/urea (including temperatures in phase II that are just below the transition from phase I to phase II), in full support of our assignment of the (3+1)-dimensional superspace group P212121(00γ) to phase II. As our phenomenological model is based on phase II and phase "III" of this incommensurate material having the same (3+1)-dimensional superspace group P212121(00γ), it follows that the new X-ray diffraction results are in full support of our phenomenological model.

Polymorphism of l-Tryptophan.

A new polymorph of l-tryptophan was prepared through crystallization from the gas phase, with structure determination carried out directly from powder XRD data augmented by periodic DFT-D calculations. The new polymorph (denoted ß) and the previously reported polymorph (denoted α) are both based on alternating hydrophilic and hydrophobic layers, but with substantially different hydrogen-bonding arrangements. The ß polymorph exhibits the energetically favourable l2-l2 hydrogen-bonding arrangement, which is unprecedented for amino acids with aromatic side chains. The specific molecular conformations adopted in the ß polymorph facilitate this hydrogen-bonding scheme while avoiding steric conflict of the side chains.

Aluminium-catalysed isocyanate trimerization, enhanced by exploiting a dynamic coordination sphere.

Main-group metals are inherently labile, hindering their use in catalysis. We exploit this lability in the synthesis of isocyanurates. For the first time we report a highly active catalyst that trimerizes alkyl, allyl and aryl isocyanates, and di-isocyanates, with low catalyst loadings under mild conditions, using a hemi-labile aluminium-pyridyl-bis(iminophenolate) complex.

Spatially resolved mapping of phase transitions in liquid-crystalline materials by X-ray birefringence imaging.

The X-ray Birefringence Imaging (XBI) technique, first reported in 2014, is a sensitive method for spatially resolved mapping of the local orientational properties of anisotropic materials. We report the first application of the XBI technique to characterize molecular orientational ordering in a liquid crystalline material, demonstrating significant potential for exploiting XBI measurements to advance structural understanding of liquid crystal phases.

A Strategy for Probing the Evolution of Crystallization Processes by Low-Temperature Solid-State NMR and Dynamic Nuclear Polarization.

Crystallization plays an important role in many areas, and to derive a fundamental understanding of crystallization processes, it is essential to understand the sequence of solid phases produced as a function of time. Here, we introduce a new NMR strategy for studying the time evolution of crystallization processes, in which the crystallizing system is quenched rapidly to low temperature at specific time points during crystallization. The crystallized phase present within the resultant "frozen solution" may be investigated in detail using a range of sophisticated NMR techniques. The low temperatures involved allow dynamic nuclear polarization (DNP) to be exploited to enhance the signal intensity in the solid-state NMR measurements, which is advantageous for detection and structural characterization of transient forms that are present only in small quantities. This work opens up the prospect of studying the very early stages of crystallization, at which the amount of solid phase present is intrinsically low.