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.

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.

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.

Exploiting in-situ solid-state NMR spectroscopy to probe the early stages of hydration of calcium aluminate cement.

We report a high-field in-situ solid-state NMR study of the hydration of CaAl2O4 (the most important hydraulic phase in calcium aluminate cement), based on time-resolved measurements of solid-state 27Al NMR spectra during the early stages of the reaction. A variant of the CLASSIC NMR methodology, involving alternate recording of direct-excitation and MQMAS 27Al NMR spectra, was used to monitor the 27Al species present in both the solid and liquid phases as a function of time. Our results provide quantitative information on the changes in the relative amounts of 27Al sites with tetrahedral coordination (the anhydrous reactant phase) and octahedral coordination (the hydrated product phases) as a function of time, and reveal significantly different kinetic and mechanistic behaviour of the hydration reaction at the different temperatures (20 °C and 60 °C) studied.

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.

Establishing the Transitory Existence of Amorphous Phases in Crystallization Pathways by the CLASSIC NMR Technique.

With the growing realization that crystallization processes may evolve through a sequence of different solid forms, including amorphous precursor phases, the development of suitable in-situ experimental probes is essential for comprehensively mapping the time-evolution of such processes. Here we demonstrate that the CLASSIC NMR (Combined Liquid- And Solid-State In-situ Crystallization NMR) strategy is a powerful technique for revealing the transitory existence of amorphous phases during crystallization processes, applying this technique to study crystallization of dl-menthol and l-menthol from their molten liquid phases. The CLASSIC NMR results provide direct insights into the conditions (including the specific time period) under which the molten liquid phase, transitory amorphous phases and final crystalline phases exist during these crystallization processes.

Insights into the Crystallization and Structural Evolution of Glycine Dihydrate by In†Situ Solid-State NMR Spectroscopy.

In situ solid-state NMR spectroscopy is exploited to monitor the structural evolution of a glycine/water glass phase formed on flash cooling an aqueous solution of glycine, with a range of modern solid-state NMR methods applied to elucidate structural properties of the solid phases present. The glycine/water glass is shown to crystallize into an intermediate phase, which then transforms to the ß polymorph of glycine. Our in situ NMR results fully corroborate the identity of the intermediate crystalline phase as glycine dihydrate, which was first proposed only very recently.

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated.

Determining Molecular Orientations in Disordered Materials from X-ray Linear Dichroism at the Iodine L1-Edge.

To demonstrate that measurements of X-ray linear dichroism are effective for determining bond orientations in disordered materials, we report the first observation of X-ray linear dichroism at the iodine L1-edge. The iodine-containing molecular solid studied in this work was the inclusion compound containing 4,4'-diiodobiphenyl guest molecules in the perhydrotriphenylene host structure. In this material, the guest substructure does not exhibit three-dimensional ordering, and thus diffraction-based techniques do not provide insights on the orientational properties of the guest molecules. Iodine L1-edge X-ray absorption spectra, recorded as a function of orientation of a single crystal of the material, exhibit significant dichroism (whereas no dichroism is observed at the iodine L2- and L3-edges). From quantitative analysis of the X-ray dichroism, the orientational properties of the C-I bonds within this material are established. The results pave the way for applying X-ray dichroism to determine molecular orientational properties of other materials, especially for partially ordered materials such as liquid crystals, confined liquids, and disordered crystalline phases, for which diffraction techniques may not be applicable.

Calculation of solid-state NMR lineshapes using contour analysis.

Two new methods for calculating lineshapes in solid-state NMR spectra are described. The first method, which we refer to as semi-analytical, allows the rapid calculation of quadrupolar central-transition lineshapes in both static and magic-angle spinning cases. The second method, which is fully numerical, allows the calculation of lineshapes resulting from any combination of interactions, including quadrupolar, dipolar and chemical shift anisotropy, and is not restricted to cases in which the principal axis systems for the different interactions are aligned. Both methods are derived from consideration of the contour lines on a plot of the resonance frequency against the Euler angles, allowing the intensity of the lineshape to be calculated at each frequency. Consequently, highly accurate lineshapes can be calculated more rapidly than previously possible, since only orientations contributing to each specific frequency are considered. For our semi-analytical method, the intensity of each point in the lineshape can be directly calculated in tens of milliseconds on a standard PC. In contrast, established methods can take several hours to calculate the same lineshape.

New in situ solid-state NMR techniques for probing the evolution of crystallization processes: pre-nucleation, nucleation and growth.

The application of in situ techniques for investigating crystallization processes promises to yield significant new insights into fundamental aspects of crystallization science. With this motivation, we recently developed a new in situ solid-state NMR technique that exploits the ability of NMR to selectively detect the solid phase in heterogeneous solid-liquid systems (of the type that exist during crystallization from solution), with the liquid phase "invisible" to the measurement. As a consequence, the technique allows the first solid particles produced during crystallization to be observed and identified, and allows the evolution of different solid phases (e.g., polymorphs) present during the crystallization process to be monitored as a function of time. This in situ solid-state NMR strategy has been demonstrated to be a powerful approach for establishing the sequence of solid phases produced during crystallization and for the discovery of new polymorphs. The most recent advance of the in situ NMR methodology has been the development of a strategy (named "CLASSIC NMR") that allows both solid-state NMR and liquid-state NMR spectra to be measured (essentially simultaneously) during the crystallization process, yielding information on the complementary changes that occur in both the solid and liquid phases as a function of time. In this article, we present new results that highlight the application of our in situ NMR techniques to successfully unravel different aspects of crystallization processes, focusing on: (i) the application of a CLASSIC NMR approach to monitor competitive inclusion processes in solid urea inclusion compounds, (ii) exploiting liquid-state NMR to gain insights into co-crystal formation between benzoic acid and pentafluorobenzoic acid, and (iii) applications of in situ solid-state NMR for the discovery of new solid forms of trimethylphosphine oxide and L-phenylalanine. Finally, the article discusses a number of important fundamental issues relating to practical aspects, the interpretation of results and the future scope of these techniques, including: (i) an assessment of the smallest size of solid particle that can be detected in in situ solid-state NMR studies of crystallization, (ii) an appraisal of whether the rapid sample spinning required by the NMR measurement technique may actually influence or perturb the crystallization behaviour, and (iii) a discussion of factors that influence the sensitivity and time-resolution of in situ solid-state NMR experiments.

Monitoring the evolution of crystallization processes by in-situ solid-state NMR spectroscopy.

Crystallization processes play a crucial role in many aspects of biological and physical sciences. Progress in deepening our fundamental understanding of such processes relies, to a large extent, on the development and application of new experimental strategies that allow direct in-situ monitoring of the process. In this paper, we give an overview of an in-situ solid-state NMR strategy that we have developed in recent years for monitoring the time-evolution of different polymorphic forms (or other solid forms) that arise as the function of time during crystallization from solution. The background to the strategy is described and several examples of the application of the technique are highlighted, focusing on both the evolution of different polymorphs during crystallization and the discovery of new polymorphs.

L-Lysine: exploiting powder X-ray diffraction to complete the set of crystal structures of the 20 directly encoded proteinogenic amino acids.

During the last 75 years, crystal structures have been reported for 19 of the 20 directly encoded proteinogenic amino acids in their natural (enantiomerically pure) form. The crystal structure is now reported for the final member of this set: L-lysine. As crystalline L-lysine has a strong propensity to incorporate water under ambient atmospheric conditions to form a hydrate phase, the pure (non-hydrate) crystalline phase can be obtained only by dehydration under rigorously anhydrous conditions, resulting in a microcrystalline powder sample. For this reason, modern powder X-ray diffraction methods have been exploited to determine the crystal structure in this final, elusive case.

Highly efficient chiral resolution of DL-arginine by cocrystal formation followed by recrystallization under preferential-enrichment conditions.

An excellent chiral symmetry-breaking spontaneous enantiomeric resolution phenomenon, denoted preferential enrichment, was observed on recrystallization of the 1:1 cocrystal of dl-arginine and fumaric acid, which is classified as a racemic compound crystal with a high eutectic ee value (>95 %), under non-equilibrium crystallization conditions. On the basis of temperature-controlled video microscopy and in situ time-resolved solid-state (13) C NMR spectroscopic studies on the crystallization process, a new mechanism of phase transition that can induce preferential enrichment is proposed.

"CLASSIC NMR": an in-situ NMR strategy for mapping the time-evolution of crystallization processes by combined liquid-state and solid-state measurements.

A new in-situ NMR strategy (termed CLASSIC NMR) for mapping the evolution of crystallization processes is reported, involving simultaneous measurement of both liquid-state and solid-state NMR spectra as a function of time. This combined strategy allows complementary information to be obtained on the evolution of both the solid and liquid phases during the crystallization process. In particular, as crystallization proceeds (monitored by solid-state NMR), the solution state becomes more dilute, leading to changes in solution-state speciation and the modes of molecular aggregation in solution, which are monitored by liquid-state NMR. The CLASSIC NMR experiment is applied here to yield new insights into the crystallization of m-aminobenzoic acid.

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.

An ENDOR and DFT analysis of hindered methyl group rotations in frozen solutions of bis(acetylacetonato)-copper(II).

ENDOR spectroscopy and DFT calculations have been used to thoroughly investigate the ligand hyperfine couplings for the bis(acetylacetonato)-copper(ii) complex [Cu(acac)2] in frozen solution. Solutions of [Cu(acac)2] were prepared under anhydrous conditions, and EPR revealed that the g and (Cu)A values were affected by traces of water present in the solvent. The ligand (H)Ai hyperfine couplings were subsequently investigated by CW and pulsed ENDOR spectroscopy. Anisotropic hyperfine couplings to the methine protons ((H)Ai = 1.35, -1.62, -2.12 MHz; a(iso) = -0.80 MHz) and smaller couplings to the fully averaged methyl group protons ((H)Ai = -0.65, 1.658, -0.9 MHz; a(iso) = 0.036 MHz) were identified by simulation of the angular selective ENDOR spectra and confirmed by DFT. Since the barrier to methyl group rotation was estimated to be ca. 5 kJ mol(-1) by DFT, rapid rotation of these -CH3 groups, even at 10 K, leads to an averaged value of (H)Ai. However, variable temperature X-band Mims ENDOR revealed an additional set of hyperfine couplings which showed a pronounced temperature dependency. Using CW Q-band ENDOR, these additional couplings were characterised by the hyperfine parameters (H)Ai = 3.45, 2.9, 2.62 MHz, a(iso) = 2.99 MHz and assigned to a hindered methyl group rotation. This hindered rotation of a sub-set of methyl groups occurs in 120° jumps, such that a large A(dip) and a(iso) component is always observed. Whilst the majority of the methyl groups undergo free rotation, a sub-set of methyl groups experience hindered rotation in frozen solution, through proton tunnelling. This hindered rotation appears to be caused by weak outer-sphere solvent interactions with the complex.

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.

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.

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.