Solid-state NMR Spectroscopic Studies Research Articles

Efficient Synthetic Access to Stable Isotope Labelled Pseudouridine Phosphoramidites for RNA NMR Spectroscopy.

Here we report the efficient synthetic access to 13C/15N-labelled pseudouridine phosphoramidites, which were incorporated into a binary H/ACA box guide RNA/product complex comprising 77 nucleotides (nts) in total and into a 75 nt E. coli tRNAGly. The stable isotope (SI) labelled pseudouridines were produced via a highly efficient chemo-enzymatic synthesis. 13C/15N labelled uracils were produced via chemical synthesis and enzymatically converted to pseudouridine 5'-monophosphate (ΨMP) by using YeiN, a Ψ-5'-monophosphate C-glycosidase. Removal of the 5'-phosphate group yielded the desired pseudouridine nucleoside (Ψ), which was transformed into a phosphoramidite building suitable for RNA solid phase synthesis. A Ψ -building block carrying both a 13C and a 15N label was incorporated into a product RNA and the complex formation with a 63 nt H/ACA box RNA could be observed via NMR. Furthermore, the SI labelled pseudouridine building block was used to determine imino proton bulk water exchange rates of a 75 nt E. coli tRNAGly CCmnm5U, identifying the TΨC-loop 5-methyluridine as a modifier of the exchange rates. The efficient synthetic access to SI-labelled Ψ building blocks will allow the solution and solid-state NMR spectroscopic studies of Ψ containing RNAs and will facilitate the mass spectrometric analysis of Ψ-modified nucleic acids.

Miscibility of Amorphous Solid Dispersions: A Rheological and Solid-State NMR Spectroscopy Study

Miscibility is critical in the prediction of stability against crystallization of amorphous solid dispersions (ASDs) in the solid state. However, currently available approaches for its determination are limited by both theoretical and practical considerations. Recently, a rheological approach guided by the polymer overlap concentration (c*) has been proposed for miscibility quantification of ASDs [J. Pharm. Sci., 112 (2023) 204−212] and shown to be useful in predicting both accelerated and long term physical stability in the absence of moisture. However, this approach can only be performed at high temperatures (slightly above the melting temperature, Tm, of drugs), and little is known about the difference in miscibility between high and low temperatures (e.g., below the glass transition temperature, Tg). Here we compare the miscibility of nifedipine (NIF)/polyvinylpyrrolidone (PVP) ASDs as determined by the rheological approach at 175°C (∼3°C above Tm of NIF) and solid state NMR (ssNMR) 1H T1 and T1ρ relaxation times at -20°C (∼66°C below Tg of NIF). Our results indicate agreement between the two methods. For low molecular weight (Mw) PVP, T1ρ measurements are more consistent with the rheological approach, while T1 measurements are closer for relatively high Mw PVP. Our findings support the use of the c* based rheological approach for inferring miscibility of deeply cooled ASDs.

Conformation of Pyroglutamated Amyloid β (3-40) and (11-40) Fibrils - Extended or Hairpin?

Amyloid β (Aβ) is a hallmark protein of Alzheimer's disease. One physiologically important Aβ variant is formed by initial N-terminal truncation at a glutamic acid position (either E3 or E11), which is subsequently cyclized to a pyroglutamate (either pE3 or pE11). Both forms have been found in high concentrations in the core of amyloid plaques and are likely of high importance in the pathology of Alzheimer's disease. However, the molecular structure of the fibrils of these variants is not entirely clear. Solid-state NMR spectroscopy studies have reported a molecular contact between Gly25 and Ile31, which would disagree with the conventional hairpin model of wildtype (WT-)Aβ1-40 fibrils, most often described in the literature. We investigated the conformation of the monomeric unit of pE3-Aβ3-40 and pE11-Aβ11-40 (and for comparison also wildtype (WT)-Aβ1-40) fibrils to find out whether the hairpin or a newly suggested extended structure dominates the structure of the Aβ monomers in these fibrils. To this end, solid-state NMR spectroscopy was applied probing the inter-residual contacts between Phe19/Leu34, Ala21/Leu34, and especially Gly25/Ile31 using suitable isotopic labeling schemes. In the second part, the flexible turn of the Aβ40 peptides was replaced by a (3-(3-aminomethyl)phenylazo)phenylacetic acid (AMPP)-based photoswitch, which can predefine the peptide conformation to either an extended (trans) or hairpin (cis) conformation. This enables simultaneous spectroscopic assessment of the conformation of the AMPP-photoswitch, allowing in situ structural investigations during fibrillation in contrast to structural techniques such as NMR spectroscopy or cryo-EM, which can only be applied to stable conformers. Both methods confirm an extended structure for the peptidic monomers in fibrils of all investigated Aβ variants. Especially the Gly25/Ile31 contact is a decisive indicator for the extended structure along with the characteristic absorption spectra of trans-AMPP-Aβ.

Synthesis and Structural Analysis of High-Silica ERI Zeolite with Spatially-Biased Al Distribution as a Promising NH3-SCR Catalyst.

Erionite (ERI) zeolite has recently attracted considerable attention for its application prospect in the selective catalytic reduction of NOx with NH3 (NH3-SCR), provided that the high-silica (Si/Al > 5.5) analog with improved hydrothermal stability can be facilely synthesized. In this work, ERI zeolites with different Si/Al ratios (4.6, 6.4, and 9.1) are synthesized through an ultrafast route, and in particular, a high-silica ERI zeolite with a Si/Al ratio of 9.1 is obtained by using faujasite (FAU) as a starting material. The solid-state 29Si MAS NMR spectroscopic study in combination with a computational simulation allows for figuring out the atomic configurations of the Al species in the three ERI zeolites. It is revealed that the ERI zeolite with the highest Si/Al ratio (ERI-9.1, where the number indicates the Si/Al ratio) exhibits a biased Al occupancy at T1 site, which is possibly due to the presence of a higher fraction of the residual potassium cations in the can cages. In contrast, the Al siting in ERI-4.6 and ERI-6.4 proves to be relatively random.

Silica Supported Organometallic IrI Complexes Enable Efficient Catalytic Methane Borylation

Catalytic C-H borylation is an attractive method for the conversion of the most abundant hydrocarbon, methane (CH4), to a mild nucleophilic building block. However, existing CH4 borylation catalysts often suffer from low turnover numbers and conversions, which is hypothesized to result from inactive metal hydride agglomerates. Herein we report that the heterogenization of a bisphosphine molecular precatalyst, [(dmpe)Ir(cod)CH3], onto amorphous silica dramatically enhances its performance, yielding a catalyst that is 12-times more efficient than the current standard for CH4 borylation. The catalyst affords over 2000 turnovers at 150 °C in 16 h with a selectivity of 91.5% for mono- vs diborylation. Higher catalyst loadings improve yield and selectivity for the monoborylated product (H3CBpin) with 82.8% yield and >99% selectivity being achieved with 1255 turnovers. X-ray absorption and dynamic nuclear polarization-enhanced solid-state NMR spectroscopic studies identify the supported precatalyst as an IrI species, and indicate that upon completion of catalysis, multinuclear Ir polyhydrides are not formed. This is consistent with the hypothesis that immobilization of the organometallic Ir species on a surface prevents bimolecular decomposition pathways. Immobilization of the homogeneous IrI fragment onto amorphous silica represents a unique and simple strategy to improve the TON and longevity of a CH4 borylation catalyst.

Trimorphic TaCrP – A diffraction and 31P solid state NMR spectroscopic study

Abstract The metal-rich phosphide TaCrP forms from the elements by step-wise solid state reaction in an alumina crucible (maximum annealing temperature 1180 K). TaCrP is trimorphic. The structural data of the hexagonal ZrNiAl high-temperature phase (space group P 6 ‾ 2 m $P\overline{6}2m$ ) was deduced from a Rietveld refinement. At room temperature TaCrP crystallizes with the TiNiSi type (Pnma, a = 623.86(5), b = 349.12(3), c = 736.78(6) pm, wR = 0.0419, 401 F 2 values, 20 variables) and shows a Peierls type transition below ca. 280 K to the monoclinic low-temperature modification (P121/c1, a = 630.09(3), b = 740.3(4), c = 928.94(4) pm, β = 132.589(5)°, wR = 0.0580, 1378 F 2 values, 57 variables). The latter phase transition is driven by pairwise Cr–Cr bond formation out of an equidistant chain in o-TaCrP. The phase transition was monitored via different analytical tools: differential scanning calorimetry, powder synchrotron X-ray diffraction, magnetic susceptibility measurements and 31P solid state NMR spectroscopy.

Solid-state NMR studies of metal ion and solvent influences upon the flexible metal-organic framework DUT-8

Within the present contribution, we describe solid-state NMR spectroscopic studies of the paddle wheel unit in the prototypic flexible MOF compound DUT-8(M) (M = Ni, Co, Zn). The 13C NMR chemical shift of these carboxylates shows a remarkable behavior. The pure 2,6-H2ndc linker carboxylates as well as DUT-8(Zn) exhibit a13C chemical shift of only about 170 ppm. In contrast, much higher values are observed for DUT-8(Ni) and especially DUT-8(Co). In the open pore state, the shift strongly depends on the solvent polarity in these two latter cases. The present contribution elucidates the reason for this solvent influence. It is concluded that the solvent mainly modifies the isotropic Fermi contact coupling constant for the excited high-spin states in DUT-8(Ni) and DUT-8(Co).

Solid-State NMR Spectroscopy Studies of Enhanced Acidity of Silica-Aluminas Based on Penta-Coordinated Aluminum Species

Solid-State NMR Spectroscopy Studies of Enhanced Acidity of Silica-Aluminas Based on Penta-Coordinated Aluminum Species

Selective Gas Uptake and Rotational Dynamics in a (3,24)-Connected Metal-Organic Framework Material.

The desolvated (3,24)-connected metal-organic framework (MOF) material, MFM-160a, [Cu3(L)(H2O)3] [H6L = 1,3,5-triazine-2,4,6-tris(aminophenyl-4-isophthalic acid)], exhibits excellent high-pressure uptake of CO2 (110 wt% at 20 bar, 298 K) and highly selective separation of C2 hydrocarbons from CH4 at 1 bar pressure. Henry's law selectivities of 79:1 for C2H2:CH4 and 70:1 for C2H4:CH4 at 298 K are observed, consistent with ideal adsorption solution theory (IAST) predictions. Significantly, MFM-160a shows a selectivity of 16:1 for C2H2:CO2. Solid-state 2H NMR spectroscopic studies on partially deuterated MFM-160-d12 confirm an ultra-low barrier (∼2 kJ mol-1) to rotation of the phenyl group in the activated MOF and a rotation rate 5 orders of magnitude slower than usually observed for solid-state materials (1.4 × 106 Hz cf. 1011-1013 Hz). Upon introduction of CO2 or C2H2 into desolvated MFM-160a, this rate of rotation was found to increase with increasing gas pressure, a phenomenon attributed to the weakening of an intramolecular hydrogen bond in the triazine-containing linker upon gas binding. DFT calculations of binding energies and interactions of CO2 and C2H2 around the triazine core are entirely consistent with the 2H NMR spectroscopic observations.

Transiently structured head domains control intermediate filament assembly

Low complexity (LC) head domains 92 and 108 residues in length are, respectively, required for assembly of neurofilament light (NFL) and desmin intermediate filaments (IFs). As studied in isolation, these IF head domains interconvert between states of conformational disorder and labile, β-strand-enriched polymers. Solid-state NMR (ss-NMR) spectroscopic studies of NFL and desmin head domain polymers reveal spectral patterns consistent with structural order. A combination of intein chemistry and segmental isotope labeling allowed preparation of fully assembled NFL and desmin IFs that could also be studied by ss-NMR. Assembled IFs revealed spectra overlapping with those observed for β-strand-enriched polymers formed from the isolated NFL and desmin head domains. Phosphorylation and disease-causing mutations reciprocally alter NFL and desmin head domain self-association yet commonly impede IF assembly. These observations show how facultative structural assembly of LC domains via labile, β-strand-enriched self-interactions may broadly influence cell morphology.

Solid-state NMR spectroscopic studies of 13C,15N,29Si-enriched biosilica from the marine diatom Cyclotella cryptica

Diatoms are algae producing micro- and nano-structured cell walls mainly containing amorphous silica. The shape and patterning of these cell walls is species-specific. Herein, the biosilica of Cyclotella cryptica, a centric marine diatom with a massive organic matrix, is studied. Solid-state NMR spectroscopy is applied to gain deeper insight into the interactions at the organic–inorganic interface of the cell walls. The various organic compounds like polysaccharides as well as proteins and long-chain polyamines (LCPAs) are detected by observation of heteronuclei like 13C and 15N whereas the silica phase is studied using 29Si NMR spectroscopy. The sensitivity of the NMR experiments is strongly enhanced by isotope-labeling of the diatoms during cultivation with 13C, 15N and 29Si. The presence of two different chitin species in the biosilica is demonstrated. This observation is supported by a monosaccharide analysis of the silica-associated organic matrix where a high amount of glucosamine is found. Moreover, the Rotational Echo Double Resonance (REDOR) experiment provides distance information for heteronuclear spins. 13C{29Si} REDOR experiments reveal proximities between different organic compounds and the silica phase. The closest contacts between silica and organic compounds appear for different signals in the 13C-chemical shift range of 40–60 ppm, the typical range for LCPAs.

Kinetics of pozzolanic reaction and carbonation in ceramic – lime system: Thermogravimetry and solid-state NMR spectroscopy study

Waste red-clay ceramic powder (RCC) is a pozzolanic material which is currently not commercially used, but high amount of “brick fraction” of construction and demolition waste may become a source for a cheap pozzolanic additive for Portland cement and lime-based binders. A sort of specific of RCC, compared to other pozzolans, is the higher content of non-reactive minerals. Pozzolanic reaction, taking place in lime-based system, is inevitably accompanied by carbonation of the lime; these two processes are concurrent with respect to the lime consumption. Products of hydration (C–S–H and calcium aluminate hydrate phases) and carbonation (CaCO3) are contributing to the strengthening of the system. The goal of this research has been to evaluate the rate and mechanism of hardening of the RCC – lime mixtures. The relative rate of pozzolanic reaction and carbonation was studied over one-year period in RCC – lime pastes by help of thermal analysis and 23Na, 27Al and 29Si Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy (MAS NMR), accompanied by porosimetry and compressive strength determination. The kinetics of lime conversion to hydration products and CaCO3 was determined by the help of thermogravimetry and described by Jander's equation. The highest rate of pozzolanic reaction, as well as the highest strength, reached mixture of 70% of RCC and 30% of lime; such high effective pozzolana content is caused by the phase composition of ceramic powder – it contains lower amount of reactive species, compared to metakaolin or other pozzolans. The formation of AlVI hydration products (AFm and AFt phases) took place within initial 3 days in all mixtures, while the content of C–S–H hydrates grown over the whole year of the experiment.

Structure and Acidity Changes in Ultra-Stable Y Zeolites During Hydrothermal Aging: A Solid-State NMR Spectroscopy Study

Structure and Acidity Changes in Ultra-Stable Y Zeolites During Hydrothermal Aging: A Solid-State NMR Spectroscopy Study

Evidence of Hydronium Formation in Water–Chabazite Zeolite Using Inelastic Neutron Scattering Experiments and ab Initio Molecular Dynamics Simulations

A combined study of inelastic neutron scattering and ab initio molecular dynamics simulations has been performed in order to study the water–acid site interaction in zeolite chabazite with a ratio Si/Al = 16 that corresponds to 2 protons/uc with two different water coverages with the number of water molecules being lower and higher than that of proton sites. These results have provided a clear picture of the water–acid site interaction, and it has been demonstrated that there are two regimens of water adsorption, which depend on the water loading. (i) At low water coverage (water/acid site ∼0.5), the main interactions between water and the zeolitic acid sites are established through hydrogen bond and there is no proton transference to water. (ii) At relatively high water loading (water/acid site ∼3), the clustering of water molecules and hydronioum cations formed by the complete transference of the zeolitic proton to the water molecules has been observed. The formation of water–hydronium clusters interacting with oxygen atoms of the zeolite framework provides the stabilization energy needed for the protonation of water molecules confined in the cavities of chabazite. These results are the experimental evidence obtained from INS of proton transfer from the zeolitic acid site and the hydronium formation and are in agreement with a previous computational study ( Phys. Chem. Chem. Phys. 2009, 11, 1702−1712) and very recent solid state NMR spectroscopy studies ( J. Am. Chem. Soc. 2019, 141, 3444−3455). The inspection of the low energy bands (translational and optic modes) and librational bands of the experimental results allows obtaining information about the H-bond network of the hydronium–water cluster.

MAS NMR on a Red/Far-Red Photochromic Cyanobacteriochrome All2699 from Nostoc.

Unlike canonical phytochromes, the GAF domain of cyanobacteriochromes (CBCRs) can bind bilins autonomously and is sufficient for functional photocycles. Despite the astonishing spectral diversity of CBCRs, the GAF1 domain of the three-GAF-domain photoreceptor all2699 from the cyanobacterium Nostoc 7120 is the only CBCR-GAF known that converts from a red-absorbing (Pr) dark state to a far-red-absorbing (Pfr) photoproduct, analogous to the more conservative phytochromes. Here we report a solid-state NMR spectroscopic study of all2699g1 in its Pr state. Conclusive NMR evidence unveils a particular stereochemical heterogeneity at the tetrahedral C31 atom, whereas the crystal structure shows exclusively the R-stereochemistry at this chiral center. Additional NMR experiments were performed on a construct comprising the GAF1 and GAF2 domains of all2699, showing a greater precision in the chromophore–protein interactions in the GAF1-2 construct. A 3D Pr structural model of the all2699g1-2 construct predicts a tongue-like region extending from the GAF2 domain (akin to canonical phytochromes) in the direction of the chromophore, shielding it from the solvent. In addition, this stabilizing element allows exclusively the R-stereochemistry for the chromophore-protein linkage. Site-directed mutagenesis performed on three conserved motifs in the hairpin-like tip confirms the interaction of the tongue region with the GAF1-bound chromophore.

Co-aromatization of methane with propane over Zn/HZSM-5: The methane reaction pathway and the effect of Zn distribution

The co-aromatization of methane with propane is investigated using Zn/HZSM-5 as the catalyst at 400 °C. The presence of methane has a pronounced effect on the product distribution in terms of improved formation of phenyl rings and substitution groups of aromatic species. Isotopic labeling and solid-state NMR spectroscopy studies reveal that the favored site for methane incorporation varies at different stages along the co-aromatization reaction, from the benzylic sites at the initial stage to the phenyl rings and then substitution groups as the reaction proceeds. SIMS spectroscopy of the involved reaction intermediates suggests the formation of C4 species over the Zn sites that are bonding to the oxygen atoms of the zeolite framework, which is supported by theoretical calculations. The interaction between Zn species and the zeolite framework is also confirmed by XAS and changes in coordination environments are identified through XANES and solid-state NMR spectroscopy. The redistribution of Zn during the reaction is observed on the surface of the zeolite support. Scanning transmission X-ray microscopy images show that Zn is rich in the inner pores compared with the external surface of the catalyst particles in the pristine catalysts. XANES and XPS spectra demonstrate that the Zn concentration increases on the external surface after the reaction, a conclusion that is further supported by the theoretical study. The Zn redistribution might be among the reasons for methane participation pathway alternation during the co-aromatization, since the Zn species located within the inner pores and on the external surface might prefer to catalyze the methane incorporation to the phenyl rings and substitution groups of the formed aromatics, respectively.

Probing Interactions of N-Donor Molecules with Open Metal Sites within Paramagnetic Cr-MIL-101: A Solid-State NMR Spectroscopic and Density Functional Theory Study.

Understanding host-guest interactions is one of the key requirements for adjusting properties in metal-organic frameworks (MOFs). In particular, systems with coordinatively unsaturated Lewis acidic metal sites feature highly selective adsorption processes. This is attributed to strong interactions with Lewis basic guest molecules. Here we show that a combination of 13C MAS NMR spectroscopy with state-of-the-art density functional theory (DFT) calculations allows one to unravel the interactions of water, 2-aminopyridine, 3-aminopyridine, and diethylamine with the open metal sites in Cr-MIL-101. The 13C MAS NMR spectra, obtained with ultrafast magic-angle spinning, are well resolved, with resonances distributed over 1000 ppm. They present a clear signature for each guest at the open metal sites. Based on competition experiments this leads to the following binding preference: water < diethylamine ≈ 2-aminopyridine < 3-aminopyridine. Assignments were done by exploiting distance sum relations derived from spin-lattice relaxation data and 13C{1H} REDOR spectral editing. The experimental data were used to validate NMR shifts computed for the Cr-MIL-101 derivatives, which contain Cr3O clusters with magnetically coupled metal centers. While both approaches provide an unequivocal assignment and the arrangement of the guests at the open metal sites, the NMR data offer additional information about the guest and framework dynamics. We expect that our strategy has the potential for probing the binding situation of adsorbate mixtures at the open metal sites of MOFs in general and thus accesses the microscopic interaction mechanisms for this important material class, which is essential for deriving structure-property relationships.

The Role of Catalyst Support, Diluent and Co-Catalyst in Chromium-Mediated Heterogeneous Ethylene Trimerisation

Sequential treatment of a previously-calcined solid oxide support (i.e. SiO2, γ-Al2O3, or mixed SiO2–Al2O3) with solutions of Cr{N(SiMe3)2}3 (0.71 wt% Cr) and a Lewis acidic alkyl aluminium-based co-catalyst (15 molar equivalents) affords initiator systems active for the oligomerisation and/or polymerisation of ethylene. The influence of the oxide support, calcination temperature, co-catalyst, and reaction diluent on both the productivity and selectivity of the immobilised chromium initiator systems have been investigated, with the best performing combination (SiO2−600, modified methyl aluminoxane-12 {MMAO-12}, heptane) producing a mixture of hexenes (61 wt%; 79% 1-hexene), and polyethylene (16 wt%) with an activity of 2403 g gCr−1 h−1. The observed product distribution is rationalised by two competing processes: trimerisation via a supported metallacycle-based mechanism and polymerisation through a classical Cossee-Arlman chain-growth pathway. This is supported by the indirect observation of two distinct chromium environments at the surface of the oxide support by a solid-state 29Si NMR spectroscopic study of the Cr{N(SiMe3)2}x/SiO2−600 pro-initiator.

Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils.

Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.

\u03b2-Sheet Structure within the Extracellular Domain of C99 Regulates Amyloidogenic Processing

Familial mutations in C99 can increase the total level of the soluble Aβ peptides produced by proteolysis, as well as the Aβ42/Aβ40 ratio, both of which are linked to the progression of Alzheimer’s disease. We show that the extracellular sequence of C99 forms β-sheet structure upon interaction with membrane bilayers. Mutations that disrupt this structure result in a significant increase in Aβ production and, in specific cases, result in an increase in the amount of Aβ42 relative to Aβ40. Fourier transform infrared and solid-state NMR spectroscopic studies reveal a central β-hairpin within the extracellular sequence comprising Y10-E11-V12 and L17-V18-F19 connected by a loop involving H13-H14-Q15. These results suggest how familial mutations in the extracellular sequence influence C99 processing and provide a structural basis for the development of small molecule modulators that would reduce Aβ production.