Combination Of Solid-state NMR Spectroscopy Research Articles

Self-assembled viologens on HOPG: solid-state NMR and AFM unravel the location of the anions.

The controlled growth of self-assembled networks on surfaces based on viologen salts is a major scientific challenge due to their unique electronic properties. The combination of solid-state NMR spectroscopy and atomic force microscopy at ambient conditions can unravel the fine organization of the supramolecular network on a graphitic surface by positioning the counter-ions relative to the viologen cation.

Site-directed cation ordering in chabazite-type AlxGa1-xPO4-34 frameworks revealed by NMR crystallography.

We report the first synthesis of the mixed-metal chabazite-type AlxGa1-xPO4-34(mim) solid solution, containing 1-methylimidazolium, mim, as structure directing agent (SDA), from the parent mixed-metal oxide solid solution, γ-(AlxGa1-x)2O3. This hitherto unreported family of materials exhibits complex disorder, arising from the possible distributions of cations over available sites, the orientation of the SDA and the presence of variable amounts of water, which provides a prototype for understanding structural subtleties in nanoporous materials. In the as-made forms of the phosphate frameworks, there are three crystallographically distinct metal sites: two tetrahedral MO4 and one octahedral MO4F2 (M = Al, Ga). A combination of solid-state NMR spectroscopy and periodic DFT calculations reveals that the octahedral site is preferentially occupied by Al and the tetrahedral sites by Ga, leading to a non-random distribution of cations within the framework. Upon calcination to the AlxGa1-xPO4-34 framework, all metal sites are tetrahedral and crystallographically equivalent in the average R3̄ symmetry. The cation distribution was explored by 31P solid-state NMR spectroscopy, and it is shown that the non-random distribution demonstrated to exist in the as-made materials would be expected to give remarkably similar patterns of peak intensities to a random distribution owing to the change in average symmetry in the calcined materials.

Importance of Nuclear Quantum Effects for Molecular Cocrystals with Short Hydrogen Bonds.

Many efforts have been recently devoted to the design and investigation of multicomponent pharmaceutical solids, such as salts and cocrystals. The experimental distinction between these solid forms is often challenging. Here, we show that the transformation of a salt into a cocrystal with a short hydrogen bond does not occur as a sharp phase transition but rather a smooth shift of the positional probability of the hydrogen atoms. A combination of solid-state NMR spectroscopy, X-ray diffraction, and diffuse reflectance measurements with density functional theory calculations that include nuclear quantum effects (NQEs) provides evidence of temperature-induced hydrogen atom shift in cocrystals with short hydrogen bonds. We demonstrate that for the predictions of the salt/cocrystal solid forms with short H-bonds, the computations have to include NQEs (particularly hydrogen nuclei delocalization) and temperature effects.

Co-factor-free aggregation of tau into seeding-competent RNA-sequestering amyloid fibrils

Pathological aggregation of the protein tau into insoluble aggregates is a hallmark of neurodegenerative diseases. The emergence of disease-specific tau aggregate structures termed tau strains, however, remains elusive. Here we show that full-length tau protein can be aggregated in the absence of co-factors into seeding-competent amyloid fibrils that sequester RNA. Using a combination of solid-state NMR spectroscopy and biochemical experiments we demonstrate that the co-factor-free amyloid fibrils of tau have a rigid core that is similar in size and location to the rigid core of tau fibrils purified from the brain of patients with corticobasal degeneration. In addition, we demonstrate that the N-terminal 30 residues of tau are immobilized during fibril formation, in agreement with the presence of an N-terminal epitope that is specifically detected by antibodies in pathological tau. Experiments in vitro and in biosensor cells further established that co-factor-free tau fibrils efficiently seed tau aggregation, while binding studies with different RNAs show that the co-factor-free tau fibrils strongly sequester RNA. Taken together the study provides a critical advance to reveal the molecular factors that guide aggregation towards disease-specific tau strains.

A crystallographic and solid-state NMR study of 1,4-disubstituted 2,5-diketopiperazines

p-Disubstituted phenyldiketopiperazines 1 (R = H), 2 (R = NO2) and 3 (R = -N(CH3)2) were synthesized and characterized by NMR in solution and IR spectroscopy. The identity of the compounds was confirmed and their fragmentation analyzed by ESI-MS and HRMS spectrometry. X-ray single crystal structures revealed that the three compounds crystallize in space groups P21 (1), Pbca (2) and P21/c (3), respectively. The solid-state structures of 1–3 were further analyzed by a combination of solid-state NMR spectroscopy and GIPAW calculations. The NMR crystallography approach was used to analyze symmetry breaking of nearly centrosymmetric molecules in 1, and disorder of piperazine groups in crystal structure of 3.

Thermal Dehydrofluorination of GaPO-34 Revealed by NMR Crystallography

Using a combination of solid-state NMR spectroscopy, powder X-ray diffraction (pXRD), thermogravimetry, and periodic density functional theory (DFT) calculations, we investigate the calcination of the chabazite-type gallophosphate, GaPO-34, prepared with either 1-methylimidazole (mim) or pyridine (py) as the structure-directing agent (SDA) and fluoride as the charge-balancing anion. We demonstrate that, prior to SDA combustion, there is an unusual low-temperature dehydrofluorination step at ∼330 °C for the mim material, but not for the py form. The DFT-derived structure for the dehydrofluorinated intermediate contains pentacoordinate Ga species with Ga–N bonds of 2.04 A to the mim nitrogen atom, in addition to four Ga–O bonds to neighboring PO4 tetrahedra. This observation is consistent with 71Ga NMR spectroscopy, which shows that one-third of the Ga is pentacoordinate with a large quadrupolar coupling constant of ∼11 MHz. Powder X-ray diffraction measured in situ on heating shows the transient appearance of a distinct crystalline phase between 325 and 425 °C before the characteristic chabazite structure is seen, which is consistent with dehydrofluorination prior to loss of the organic SDA. No such dehydrofluorinated intermediate structure is observed for the py form of GaPO-34, which is ascribed to the lower pKa of pyridinium relative to 1-methylimidazolium.

Structural characterization of the D290V mutation site in hnRNPA2 low-complexity–domain polymers

Human genetic studies have given evidence of familial, disease-causing mutations in the analogous amino acid residue shared by three related RNA binding proteins causative of three neurological diseases. Alteration of aspartic acid residue 290 of hnRNPA2 to valine is believed to predispose patients to multisystem proteinopathy. Mutation of aspartic acid 262 of hnRNPA1 to either valine or asparagine has been linked to either amyotrophic lateral sclerosis or multisystem proteinopathy. Mutation of aspartic acid 378 of hnRNPDL to either asparagine or histidine has been associated with limb girdle muscular dystrophy. All three of these aspartic acid residues map to evolutionarily conserved regions of low-complexity (LC) sequence that may function in states of either intrinsic disorder or labile self-association. Here, we present a combination of solid-state NMR spectroscopy with segmental isotope labeling and electron microscopy on the LC domain of the hnRNPA2 protein. We show that, for both the wild-type protein and the aspartic acid 290-to-valine mutant, labile polymers are formed in which the LC domain associates into an in-register cross-β conformation. Aspartic acid 290 is shown to be charged at physiological pH and immobilized within the polymer core. Polymers of the aspartic acid 290-to-valine mutant are thermodynamically more stable than wild-type polymers. These observations give evidence that removal of destabilizing electrostatic interactions may be responsible for the increased propensity of the mutated LC domains to self-associate in disease-causing conformations.

Mixtures of Alcohols and Water confined in Mesoporous Silica: A Combined Solid-State NMR and Molecular Dynamics Simulation Study

The behavior of mixtures of 1-octanol with water with different molar ratios confined inside the mesoporous silica SBA-15 was investigated by a combination of solid-state NMR spectroscopy and molec...

Structure determination of a partially ordered layered silicate material with an NMR crystallography approach.

Structure determination of layered materials can present challenges for conventional diffraction methods due to the fact that such materials often lack full three-dimensional periodicity since adjacent layers may not stack in an orderly and regular fashion. In such cases, NMR crystallography strategies involving a combination of solid-state NMR spectroscopy, powder X-ray diffraction, and computational chemistry methods can often reveal structural details that cannot be acquired from diffraction alone. We present here the structure determination of a surfactant-templated layered silicate material that lacks full three-dimensional crystallinity using such an NMR crystallography approach. Through a combination of powder X-ray diffraction and advanced 29Si solid-state NMR spectroscopy, it is revealed that the structure of the silicate layer of this layered silicate material templated with cetyltrimethylammonium surfactant cations is isostructural with the silicate layer of a previously reported material referred to as ilerite, octosilicate, or RUB-18. High-field 1H NMR spectroscopy reveals differences between the materials in terms of the ordering of silanol groups on the surfaces of the layers, as well as the contents of the inter-layer space.

A Multinuclear NMR Study of Six Forms of AlPO-34: Structure and Motional Broadening

We report a study of the CHA-type aluminophosphate AlPO-34, prepared with six different structure-directing agents (SDAs): piperidine (pip), morpholine (mor), pyridine (pyr), 1,4,8,11-tetraazacyclotetradecane (cyclam), 1,3-dimethylimidazolium (dmim) chloride, and 1-ethyl-3-methylimidazolium (emim) bromide. Using a combination of solid-state NMR spectroscopy, periodic density functional theory (DFT) calculations, and synchrotron X-ray diffraction, we show that, even in crystallographically well-ordered materials such as AlPO-34 with dmim as the SDA, local disorder may be present. For such disordered structures, where it is challenging to use DFT to assign NMR spectra, we show that the 31P isotropic chemical shift can be predicted accurately using the mean P–O bond length and P–O–Al bond angle, in an extension of previous work. Variable-temperature 27Al NMR reveals the presence of microsecond-time scale dynamics in all forms of AlPO-34, with two different motional regimes observed, depending on whether stru...

Mixtures of Isobutyric Acid and Water Confined in Cylindrical Silica Nanopores Revisited: A Combined Solid-State NMR and Molecular Dynamics Simulation Study

The phase behavior of a mixture of isobutyric acid and water confined in mesoporous SBA-15 silica material is studied by a combination of solid-state NMR spectroscopy and molecular dynamics (MD) simulations. The combination of these two techniques shows that the iBA-rich phase is close to the pore wall and the water-rich phase is in the center of the pores. The MD simulations reveal that this surprising phase behavior is mainly the result of the minimization of the hydrogen-bonding enthalpy. Moreover, the simulations show also that upon increasing temperature the relative water concentration increases at the pore surface, which is attributed to entropic contributions which lead to a more thorough miscibility. These results solve a long-standing problem of the microphase separation inside these materials.

Hydroxyproline Ring Pucker Causes Frustration of Helix Parameters in the Collagen Triple Helix.

Collagens, the most abundant proteins in mammals, are defined by their triple-helical structures and distinctive Gly-Xaa-Yaa repeating sequence, where Xaa is often proline and Yaa, hydroxyproline (Hyp/O). It is known that hydroxyproline in the Yaa position stabilises the triple helix, and that lack of proline hydroxylation in vivo leads to dysfunctional collagen extracellular matrix assembly, due to a range of factors such as a change in hydration properties. In addition, we note that in model peptides, when Yaa is unmodified proline, the Xaa proline has a strong propensity to adopt an endo ring conformation, whilst when Yaa is hydroxyproline, the Xaa proline adopts a range of endo and exo conformations. Here we use a combination of solid-state NMR spectroscopy and potential energy landscape modelling of synthetic triple-helical collagen peptides to understand this effect. We show that hydroxylation of the Yaa proline causes the Xaa proline ring conformation to become metastable, which in turn confers flexibility on the triple helix.

Quantitative Analysis of the Water Occupancy around the Selectivity Filter of a K+ Channel in Different Gating Modes

Recovery in K(+) channels, that is, the transition from the inactivated nonconductive selectivity filter conformation toward the conductive conformation, occurs on a time scale of the order of seconds, which is astonishingly long, given that the structural differences among the filter conformations are faint (<1 Å). Computational studies and electrophysiological measurements suggested that buried water molecules bound behind the selectivity filter are at the origin of the slowness of recovery in K(+) channels. Using a combination of solid-state NMR spectroscopy (ssNMR) and long molecular dynamics simulations, we sketch a high-resolution map of the spatial and temporal distribution of water behind the selectivity filter of a membrane-embedded K(+) channel in two different gating modes. Our study demonstrates that buried water molecules with long residence times are spread all along the rear of the inactivated filter, which explains the recovery kinetics. In contrast, the same region of the structure appears to be dewetted when the selectivity filter is in the conductive state. Using proton-detected ssNMR on fully protonated channels, we demonstrate the presence of a pathway that allows for the interchange of buried and bulk water, as required for a functional influence of buried water on recovery and slow inactivation. Furthermore, we provide direct experimental evidence for the presence of additional ordered water molecules that surround the filter and that are modulated by the channel's gating mode.

β-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel

The voltage-dependent anion channel (VDAC) is themajor protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined asa 19-stranded β-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's β-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic β-barrel states which underlie VDAC closure. Our results also indicate that β-barrel channels are intrinsically flexible.

31P and 13C solid‐state NMR spectroscopy to study collagen synthesis and biomineralization in polymer‐based bone implants

A combination of solid-state NMR spectroscopy and MRI was used to evaluate the formation of extracellular matrix in poly(D,L-lactide-co-glycolide) (PLGA) bone implants. Porous PLGA scaffolds were implanted into rat tibiae and analysed after 2, 4 or 8 weeks. MRI clearly delineated the implants within the cancellous bone. Differences in the trabecular structure of the implanted material and native bone were demonstrated. In addition, implants were analyzed by solid-state NMR spectroscopy under magic angle spinning. (13)C NMR spectra showed the unambiguous signature of collagen formed in the scaffolds, but also the characteristic signals of the PLGA matrix, indicating that resorption was not complete after 8 weeks. Furthermore, (31)P NMR spectroscopy detected the inorganic component of the matrix, which is composed of bioapatite. (31)P NMR spectra were quantified and this analysis revealed that the amount of inorganic extracellular matrix formed de novo was significantly lower than in native bone. This demonstrates that solid-state NMR spectroscopy, in particular in combination with MRI, can provide useful information on the composition and structure of the extracellular matrix, and serve as a tool to evaluate the quality of tissue engineering strategies.

Synthesis and characterization of bis(trialkoxysilymethyl)arenes from related bis(trichlorosilylmethyl)arenes. Comparisons between some organosilicate xerogel materials derived from both

A series of bis(trialkoxysilylmethyl)aryl compounds1–17 {[(RO) 3 SiCH 2 ] 2 Ar, R=Me, Et, Pr , Bu, Ar=1,4-C 6 H 4 ; R=Et, Pr, Bu, Ar=1,4-C 6 H 2 Me 2 -2,6; R=Et, Pr, Bu, Ar=1,4-C 6 Me 4 -2,3,5,6 ; R=Et, Pr, Bu, Ar=1,3-C 6 H 4 ; R=Bu, Ar=1,2-C 6 H 4 ; R=Et, Pr, Bu, Ar=9,10-C 14 H 8 } prepared from the related bis(trichlorosilylmethyl)aryl compounds and characterised by 1 H, 13 C and 29 Si NMR and IR spectroscopy, and high resolution mass spectrometry. The X-ray crystal structures of two of the bis(trichlorosilylmethyl)aryl precursor compounds are reported. Organosilicate xerogels prepared from the precursors 2,7 and 12 are discussed. These have been studied by a combination of solid state NMR spectroscopy, scanning electron microscopy (one case) and nitrogen sorption porosimetry and their properties compared with those of xerogels derived from related bis(trichlorosilylmethyl)arenes.