Interplay of non-covalent interactions in ribbon-like guanosine self-assembly : a NMR crystallography study

A NMR crystallography study shows how intermolecular NH...O, NH...N, OH...N, OH...O and CH–π interactions stabilize the ribbon-like supramolecular structures of three different guanosine derivatives; guanosine dihydrate (G), 3/, 5/–O– dipropanolyl deoxyguanosine (dGC(3)2) and 3/, 5/ –O– isopropylideneguanosine hemihydrate (Gace). Experimental solid-state 1H NMR spectra obtained at 20 T using fast Magic-Angle Spinning (MAS), here at 75 kHz, are presented for a dihydrate of G. For each guanosine derivative, the role of specific interactions is probed by means of NMR chemical shifts calculated using the Density Functional Theory (DFT) Gauge-Including Projector-Augmented Wave (GIPAW) approach for the full crystal and extracted isolated single molecules. Specifically, the isolated molecule to full crystal transformations result in net changes in the GIPAW calculated 1H NMR chemical shifts of up to 8 ppm for OH...O, up to 6.5 ppm for NH...N and up to 4.6 ppm for NH...O hydrogen bonds; notably, the presence of water molecules in G and Gace reinforces the molecular stacking through strong OH...O hydrogen bonds. The sugar conformations are markedly different in G, dG(C3)2 and Gace, and it is shown that the experimental 13C solid-state NMR chemical shift at the C8 position is a reliable indicator of a ‘syn’ (> 135 ppm) or ‘anti’ (< 135 ppm) conformer

Determination of a complex crystal structure in the absence of single crystals : analysis of powder X-ray diffraction data, guided by solid-state NMR and periodic DFT calculations, reveals a new 2′-deoxyguanosine structural motif

Derivatives of guanine exhibit diverse supramolecular chemistry, with a variety of distinct hydrogen-bonding motifs reported in the solid state, including ribbons and quartets, which resemble the G-quadruplex found in nucleic acids with sequences rich in guanine. Reflecting this diversity, the solid-state structural properties of 3′,5′-bis-O-decanoyl-2′-deoxyguanosine, reported in this paper, reveal a hydrogen-bonded guanine ribbon motif that has not been observed previously for 2′-deoxyguanosine derivatives. In this case, structure determination was carried out directly from powder XRD data, representing one of the most challenging organic molecular structures (a 90-atom molecule) that has been solved to date by this technique. While specific challenges were encountered in the structure determination process, a successful outcome was achieved by augmenting the powder XRD analysis with information derived from solid-state NMR data and with dispersion-corrected periodic DFT calculations for structure optimization. The synergy of experimental and computational methodologies demonstrated in the present work is likely to be an essential feature of strategies to further expand the application of powder XRD as a technique for structure determination of organic molecular materials of even greater complexity in the future

G4-Quartet·M+Borate Hydrogels

The ability to modulate the physical properties of a supramolecular hydrogel may be beneficial for biomaterial and biomedical applications. We find that guanosine (G 1), when combined with 0.5 equiv of potassium borate, forms a strong, self-supporting hydrogel with elastic moduli >10 kPa. The countercation in the borate salt (MB(OH)4) significantly alters the physical properties of the hydrogel. The gelator combination of G 1 and KB(OH)4 formed the strongest hydrogel, while the weakest system was obtained with LiB(OH)4, as judged by 1H NMR and rheology. Data from powder XRD, 1H double-quantum solid-state magic-angle spinning (MAS) NMR and small-angle neutron scattering (SANS) were consistent with a structural model that involves formation of borate dimers and G4·K+ quartets by G 1 and KB(OH)4. Stacking of these G4·M+ quartets into G4-nanowires gives a hydrogel. We found that the M+ cation helps stabilize the anionic guanosine-borate (GB) diesters, as well as the G4-quartets. Supplementing the standard gelator mixture of G 1 and 0.5 equiv of KB(OH)4 with additional KCl or KNO3 increased the strength of the hydrogel. We found that thioflavin T fluoresces in the presence of G4·M+ precursor structures. This fluorescence response for thioflavin T was the greatest for the K+ GB system, presumably due to the enhanced interaction of the dye with the more stable G4·K+ quartets. The fluorescence of thioflavin T increased as a function of gelator concentration with an increase that correlated with the system’s gel point, as measured by solution viscosit

Magic-angle spinning NMR spectroscopy provides insight into the impact of small molecule uptake by G-quartet hydrogels

Small molecule guests influence the functional properties of supramolecular hydrogels. Molecular-level understanding of such sol-gel compositions and structures is challenging due to the lack of long-range order and inherently heterogeneous sol-gel interface. In this study, insight into the uptake process of biologically relevant small molecules into guanosine-quartet(G4) borate hydrogels is obtained by gel-state magic-angle spinning (MAS) NMR spectroscopy. G4∙K+ borate hydrogel can absorb up to 0.3 equivalent of cationic methylene blue (MB) without a significant disruption of the G4 fibrils that make up the gel, whereas the addition of over 0.3 equivalents of MB to the same gel leads to a gel-to-sol transition. The gel-to-sol transition process is characterized ex situ by analyzing and comparing the 1H and 11B MAS NMR spectra acquired before and after the MB uptake. In particular, 11B isotropic chemical shifts and quadrupole interactions were determined by analyzing the 11B MAS NMR spectra acquired at different magnetic fields, 11.7 T, 14.1 T and 20 T, which enable the different local bonding environments of borate anions in sol- and gel domains to be distinguished and identified. By comparison, uptake of heterocyclic molecules such as adenine, cytosine and 1-methylthymine into G4∙Na+ borate hydrogels lead to stiff and clear gels while increasing the solubility of the nucleobases as compared to the solubility of the same compounds in water. G4∙Na+ gel can uptake one equiv. of adenine with minimal disruption to the sol-gel framework, thus enhancing the adenine solubility up to an order of magnitude as compared to water. Combined multinuclear (1H, 11B and 23Na) NMR spectroscopy analysis and vial inversion tests revealed that the nucleobases are embedded into pores of the sol phase rather than being closely interacting with the G-4 fibrils that make up the gel phase. These results indicate that G-4 hydrogels have potential applications as carrier systems for small molecules. Gel-state MAS NMR spectroscopy can be used to gain insight into host-guest interactions in complex heterogeneous sol-gel systems, which is often difficult to obtain from the conventional techniques such as X-ray scattering, electron microscopy and optical spectroscopy

One-Year Water-Stable and Porous Bi(III) Halide Semiconductor with Broad-Spectrum Antibacterial Performance

Hybrid metal halide semiconductors are a unique family of materials with immense potential for numerous applications. For this to materialize, environmental stability and toxicity deficiencies must be simultaneously addressed. We report here a porous, visible light semiconductor, namely, (DHS)Bi2I8 (DHS = [2.2.2] cryptand), which consists of nontoxic, earth-abundant elements, and is water-stable for more than a year. Gas- and vapor-sorption studies revealed that it can selectively and reversibly adsorb H2O and D2O at room temperature (RT) while remaining impervious to N2 and CO2. Solid-state NMR measurements and density functional theory (DFT) calculations verified the incorporation of H2O and D2O in the molecular cages, validating the porous nature. In addition to porosity, the material exhibits broad band-edge light emission centered at 600 nm with a full width at half-maximum (fwhm) of 99 nm, which is maintained after 6 months of immersion in H2O. Moreover, (DHS)Bi2I8 exhibits bacteriocidal action against three Gram-positive and three Gram-negative bacteria, including antibiotic-resistant strains. This performance, coupled with the recorded water stability and porous nature, renders it suitable for a plethora of applications, from solid-state batteries to water purification and disinfection

Full-genome sequencing as a basis for molecular epidemiology studies of bluetongue virus in India

Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV). Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp.) and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV ‘topotype’. However, genome-segment 5 (Seg-5) encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03) are closely related (&gt;99% identity) to a South African BTV-2 vaccine-strain (western topotype). Similarly BTV-10 isolates (IND2003/06; IND2005/04) show &gt;99% identity in all genome segments, to the prototype BTV-10 (CA-8) strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of ‘live’ South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies

An NMR crystallography study of the hemihydrate of 2′, 3′-O-isopropylidineguanosine

An NMR crystallography study of the hemihydrate of 2′, 3′-O-isopropylidineguanosine (Gace) is presented, together with powder X-ray diffraction and thermogravimetric analysis. 1H double-quantum and 14N–1H HMQC spectra recorded at 850 MHz and 75 kHz MAS (using a JEOL 1 mm probe) are presented together with a 1H–13C refocused INEPT spectrum recorded at 500 MHz and 12.5 kHz MAS using eDUMBO-1221H homonuclear decoupling. NMR chemical shieldings are calculated using the GIPAW (gauge-including projector augmented wave) method; good two-dimensional agreement between calculation and experiment is observed for 13C and 1H chemical shifts for directly bonded CH and CH3 peaks. There are two Gace molecules in the asymmetric unit cell: differences in specific 1H chemical shifts are rationalised in terms of the strength of CH-π and intermolecular hydrogen bonding interactions

A fast magic-angle spinning three-dimensional NMR experiment for simultaneously probing H-H and N-H proximities in solids

A fast magic-angle spinning (MAS) solid-state NMR experiment is presented that combines 1H Double-Quantum (DQ) and 14N-1H HMQC (Heteronuclear Multiple-Quantum Coherence) pulse-sequence elements, so as to simultaneously probe H-H and N-H proximities in molecular solids. The proposed experiment can be employed in both two-dimensional (2D) and three-dimensional (3D) versions: firstly, a 2D 14N HMQC-filtered 1H-DQ experiment provides specific DQ-SQ correlation peaks for proton pairs that are in close proximities to the nitrogen sites, thereby achieving spectral filtration. Secondly, a proton-detected three-dimensional (3D) 1H(DQ)-14N(SQ)-1H(SQ) experiment correlates 1H(SQ)-1H(DQ) chemical shifts with 14N shifts such that longer range N…H-H correlations are observed between protons and nitrogen atoms with internuclear NH distances exceeding 3 Å. Both 2D and 3D versions of the proposed experiment are demonstrated for an amino acid hydrochloride salt, L-histidine.HCl.H2O, and a DNA nucleoside, guanosine.2H2O. In the latter case, the achieved spectral filtration ensures that DQ cross peaks are only observed for guanine NH and CH8 1H resonances and not ribose and water 1H resonances, thus providing insight into the changes in the solid-state structure of this hydrate that occur over time – significant changes are observed in the NH and NH2 1H chemical shifts as compared to the freshly recrystallized sample previously studied by Reddy et al, Cryst. Growth Des. 15, 5945, 2015

Combined maximum-quantum and DOSY 3D experiments provide enhanced resolution for small molecules in mixtures

International audienceWe illustrate here as the combination of high-order maximum-quantum (MaxQ) and Diffusion-Ordered SpectroscopY (DOSY) NMR experiments in a 3D layout allows superior resolution for crowded NMR spectra. Non-uniform sampling (NUS) allows compressing the experimental time effectively to reasonable durations. Because diffusion effects were encoded within multiple-quantum co-herences, increased sensitivity to magnetic field gradients is observed, requiring compensation for convection effects. The experiment was demonstrated on the spectra of a mix of small polyaromatic molecules. Specifically, in the case analyzed, the experiment provided an extreme simplification through the MaxQDOSY-MaxQ projection plane that presents one peak per molecule

Discerning the degenerate transitions of scalar coupled <SUP>1</SUP>H NMR spectra: correlation and resolved techniques at higher quantum

The blend of spin topological filtering and the spin state selective detection of single quantum transitions by the two dimensional multiple quantum-single quantum correlation and higher quantum resolved techniques have been employed for simplifying the complexity of scalar coupled 1H NMR spectra. The conventional two dimensional COSY and TOCSY experiments, though identify the coupled spin networks, fail to differentiate them due to severe overlap of transitions. Non-selective excitation of homonuclear higher quantum of protons results in filtering of spin systems irrespective of their spin topologies. The spin state selection by passive 19F spins provides fewer transitions in each cross section of the single quantum dimension simplifying the analyses of the complex spectra. The degenerate single quantum transitions are further discerned by spin selective double and/or triple quantum resolved experiments that mimic simultaneous heteronuclear and selective homonuclear decoupling in the higher quantum dimension. The techniques aided the determination of precise values of spectral parameters and relative signs of the couplings