Multidimensional Solid-state NMR Spectroscopy Research Articles

Enhancing Spectrometer Performance with Unsupervised Machine Learning.

Solid-state NMR spectroscopy (SSNMR) is a powerful technique to probe structural and dynamic properties of biomolecules at an atomic level. Modern SSNMR methods employ multidimensional pulse sequences requiring data collection over a period of days to weeks. Variations in signal intensity or frequency due to environmental fluctuation introduce artifacts into the spectra. Therefore, it is critical to actively monitor instrumentation subject to fluctuations. Here, we demonstrate a method rooted in the unsupervised machine learning algorithm principal component analysis (PCA) to evaluate the impact of environmental parameters that affect sensitivity, resolution and peak positions (chemical shifts) in multidimensional SSNMR protein spectra. PCA loading spectra illustrate the unique features associated with each drifting parameter, while the PCA scores quantify the magnitude of parameter drift. This is demonstrated both for double (HC) and triple resonance (HCN) experiments. Furthermore, we apply this methodology to identify magnetic field B0 drift, and leverage PCA to "denoise" multidimensional SSNMR spectra of the membrane protein, EmrE, using several spectra collected over several days. Finally, we utilize PCA to identify changes in B1 (CP and decoupling) and B0 fields in a manner that we envision could be automated in the future. Overall, these approaches enable improved objectivity in monitoring NMR spectrometers, and are also applicable to other forms of spectroscopy.

Unveiling the Brønsted acid mechanism for Meerwein–Ponndorf–Verley reduction in methanol conversion over ZSM-5

The conversion of methanol over zeolites offers a sustainable alternative for fuels and chemicals production. However, a complete understanding of the competing reaction pathways, particularly those leading to C-C bond formation, remains elusive. This work presents a novel mechanism for selective methanol conversion in ZSM-5 zeolites, involving a Brønsted acid site (BAS)-mediated Meerwein–Ponndorf–Verley (MPV) reduction pathway. Employing a multidimensional solid-state NMR spectroscopy combined with isotopic labeling and theoretical calculations, we identify this pathway for acetaldehyde reduction with methanol, directly contributing to ethene formation. This mechanism, involving carbenium ion intermediates like 1-hydroxyethane or 1-methoxyethane ions, contrasts with the well-established Lewis acid-catalyzed MPV process. Based on reactant adsorption modes, we propose two distinct reaction routes for BAS-MPV reduction, bridging the gap between direct and hydrocarbon pool mechanisms in methanol conversion. We further demonstrate the applicability of this pathway to acetone, highlighting its broader role in the early stages of the reaction.

Exploiting heterogeneous time scale of dynamics to enhance 2D HETCOR solid-state NMR sensitivity.

Multidimensional solid-state NMR spectroscopy plays a significant role in offering atomic-level insights into molecular systems. In particular, heteronuclear chemical shift correlation (HETCOR) experiments could provide local chemical and structural information in terms of spatial heteronuclear proximity and through-bond connectivity. In solid state, the transfer of magnetization between heteronuclei, a key step in HETCOR experiments, is usually achieved using cross-polarization (CP) or insensitive nuclei enhanced by polarization transfer (INEPT) depending on the sample characteristics and magic-angle-spinning (MAS) frequency. But, for a multiphase system constituting molecular components that differ in their time scales of mobilities, CP efficiency is pretty low for mobile components because of the averaging of heteronuclear dipolar couplings whereas INEPT is inefficient for immobile components due to the short T2 and can yield through-space connectivity due to strong proton spin diffusion for immobile components especially under moderate spinning speeds. Herein, in this study we present two 2D pulse sequences that enable the sequential acquisition of 13C/1H HETCOR NMR spectra for the rigid and mobile components by taking full advantage of the abundant proton magnetization in a single experiment with barely increasing the overall experimental time. In particular, the 13C-detected HETCOR experiment could be applied under slow MAS conditions, where a multiple-pulse sequence is typically employed to enhance 1H spectral resolution in the indirect dimension. In contrast, the 1H-detected HETCOR experiment should be applied under ultrafast MAS, where CP and heteronuclear nuclear Overhauser effect (NOE) polarization transfer are combined to enhance 13C signal intensities for mobile components. These pulse sequences are experimentally demonstrated on two model systems to obtain 2D 13C/1H chemical shift correlation spectra of rigid and mobile components independently and separately. These pulse sequences can be used for dynamics based spectral editing and resonance assignments. Therefore, we believe the proposed 2D HETCOR NMR pulse sequences will be beneficial for the structural studies of heterogeneous systems containing molecular components that differ in their time scale of motions for understanding the interplay of structures and properties.

Characterization of Silicon Nanocrystal Surfaces by Multidimensional Solid-State NMR Spectroscopy

The chemical and photophysical properties of silicon nanocrystals (Si NCs) are strongly dependent on the chemical composition and structure of their surfaces. Here we use fast magic angle spinning (MAS) and proton detection to enable the rapid acquisition of dipolar and scalar 2D 1H–29Si heteronuclear correlation (HETCOR) solid-state NMR spectra and reveal a molecular picture of hydride-terminated and alkyl-functionalized surfaces of Si NCs produced in a nonthermal plasma. 2D 1H–29Si HETCOR and dipolar 2D 1H–1H multiple-quantum correlation spectra illustrate that resonances from surface mono-, di-, and trihydride groups cannot be resolved, contrary to previous literature assignments. Instead the 2D NMR spectra illustrate that there is large distribution of 1H and 29Si chemical shifts for the surface hydride species in both the as-synthesized and functionalized Si NCs. However, proton-detected 1H–29Si refocused INEPT experiments can be used to unambiguously differentiate NMR signals from the different surf...

Properties of Water Confined in Periodic Mesoporous Organosilicas: Nanoimprinting the Local Structure.

The properties of materials confined in porous media are important in scientific and technological aspects. Topology, size, and surface polarity of the pores play a critical role in the confinement effects, however, knowledge regarding the guest-pore interface structure is still lacking. Herein, we show that the molecular mobility of water confined in periodic mesoporous organosilicas (PMOs) is influenced by the polarity of the organic moiety. Multidimensional solid-state NMR spectroscopy directly probes the spatial arrangement of water inside the pores, showing that water interacts either with only the silicate layer or with both silicate and organic layers depending on the alternating surface polarity. A modulated and a uniform pore filling mode are proposed for different types of PMOs.

Cell-free expression, purification, and membrane reconstitution for NMR studies of the nonstructural protein 4B from hepatitis C virus.

We describe the expression of the hepatitis C virus nonstructural protein 4B (NS4B), which is an integral membrane protein, in a wheat germ cell-free system, the subsequent purification and characterization of NS4B and its insertion into proteoliposomes in amounts sufficient for multidimensional solid-state NMR spectroscopy. First spectra of the isotopically [(2)H,(13)C,(15)N]-labeled protein are shown to yield narrow (13)C resonance lines and a proper, predominantly α-helical fold. Clean residue-selective leucine, isoleucine and threonine-labeling is demonstrated. These results evidence the suitability of the wheat germ-produced integral membrane protein NS4B for solid-state NMR. Still, the proton linewidth under fast magic angle spinning is broader than expected for a perfect sample and possible causes are discussed.

ChemInform Abstract: Past and Future Solid‐State NMR Spectroscopy Studies at the Convergence Point Between Biology and Materials Research

AbstractReview: [80 refs.

Multidimensional Solid-State NMR of Functional Chemotaxis Receptor Signaling Complexes

Bacterial chemotaxis receptors serve as an ideal model system for elucidating molecular mechanisms of transmembrane signaling, due to the experimental accessibility and established biochemical characterization of these proteins. A gap in the structural understanding of bacterial chemotaxis is present between electron microscopy of the intact arrays of receptor complexes found in cells and high-resolution crystal structures of individual proteins and truncated complexes. To bridge this gap we have initiated multidimensional solid-state NMR spectroscopy studies of a kinase-active ternary complex composed of the soluble 30 kDa cytoplasmic fragment (CF) of the aspartate chemoreceptor, the 70 kDa histidine kinase CheA, and the 18 kDa adaptor protein CheW. We prepared uniformly 13C & 15N labeled CF and obtained both homonuclear and heteronuclear correlation spectra of frozen and unfrozen complexes.The initial data indicates that such experiments are feasible on this functional multi-protein complex. A number of narrow resonances with sub-ppm linewidths are observed in spectra of both frozen and unfrozen samples, and both states exhibit sufficient signal-to-noise for acquiring multidimensional spectra. Overall, the spectra demonstrate the strongly overlapping resonances expected for an alpha-helical 30 kDa protein, which suggests selective labeling for future measurements of structural constraints. For these samples containing uniformly labeled receptor fragment, comparison with predicted chemical shift spectra are being used to test the current structural model. Comparisons of frozen and unfrozen spectra are also being used to assess the presence of static disorder or dynamics in the side chain and backbone resonances. The goal for uniformly labeled receptor samples is to compare spectral properties of both signaling states to gain insight into possible differences in structure and dynamics.This research supported by NIH grant GM085288.

Establishing a molecular relationship between chondritic and cometary organic solids

Multidimensional solid-state NMR spectroscopy is used to refine the identification and abundance determination of functional groups in insoluble organic matter (IOM) isolated from a carbonaceous chondrite (Murchison, CM2). It is shown that IOM is composed primarily of highly substituted single ring aromatics, substituted furan/pyran moieties, highly branched oxygenated aliphatics, and carbonyl groups. A pathway for producing an IOM-like molecular structure through formaldehyde polymerization is proposed and tested experimentally. Solid-state (13)C NMR analysis of aqueously altered formaldehyde polymer reveals considerable similarity with chondritic IOM. Carbon X-ray absorption near edge structure spectroscopy of formaldehyde polymer reveals the presence of similar functional groups across certain Comet 81P/Wild 2 organic solids, interplanetary dust particles, and primitive IOM. Variation in functional group concentration amongst these extraterrestrial materials is understood to be a result of various degrees of processing in the parent bodies, in space, during atmospheric entry, etc. These results support the hypothesis that chondritic IOM and cometary refractory organic solids are related chemically and likely were derived from formaldehyde polymer. The fine-scale morphology of formaldehyde polymer produced in the experiment reveals abundant nanospherules that are similar in size and shape to organic nanoglobules that are ubiquitous in primitive chondrites.

A Well‐Defined Silica‐Supported Lanthanum Bis(phosphinimino)methanide

AbstractGrafting of the bis(phosphinimino)methanide complex [La{CH(PPh2NSiMe3)2}{N(SiHMe2)2}2] (1) onto dehydroxylated silica (SiO2‐700) affords material 2. Full characterization of this material by infrared spectroscopy, elemental analysis, and multinuclear, multidimensional solid‐state NMR spectroscopy showed formation of well‐defined bis(phosphinimino)methanide amido surface species, [(≡SiO)La{CH(PPh2NSiMe3)2}{N(SiHMe2)2}], along with [≡SiOSiHMe2] sites.

Conformation of a Seven‐Helical Transmembrane Photosensor in the Lipid Environment

Break on through: High-resolution multidimensional solid-state NMR spectroscopy was used to refine the molecular conformation of a seven-helical transmembrane photoreceptor in lipids (see picture, right). H/D exchange experiments (see picture, left; black spectrum: H2O, red spectrum: D2O) reveal the solvent-exposed surface of the protein, which is asymmetrically positioned in the bilayer.

ChemInform Abstract: The Structure, Dynamics, and Orientation of Antimicrobial Peptides in Membranes by Multidimensional Solid-State NMR Spectroscopy

Abstract Linear peptide antibiotics have been isolated from amphibians, insects and humans and used as templates to design cheaper and more potent analogues for medical applications. Peptides such as cecropins or magainins are ≤40 amino acids in length. Many of them have been prepared by solid-phase peptide synthesis with isotopic labels incorporated at selected sites. Structural analysis by solid-state NMR spectroscopy and other biophysical techniques indicates that these peptide antibiotics strongly interact with lipid membranes. In bilayer environments they exhibit amphipathic α-helical conformations and alignments of the helix axis parallel to the membrane surface. This contrasts the transmembrane orientations observed for alamethicin or gramicidin A. Models that have been proposed to explain the antibiotic and pore-forming activities of membrane-associated peptides, as well as other experimental results, include transmembrane helical bundles, wormholes, carpets, detergent-like effects or the in-plane diffusion of peptide-induced bilayer instabilities.

多核種・多次元固体NMR分光法の鉱物・メルトへの応用

多核種・多次元固体NMR分光法の鉱物・メルトへの応用

多核種・多次元固体NMR分光法の魅力 –含水高圧鉱物・含水アルミノケイ酸塩ガラスを例に–

多核種・多次元固体NMR分光法の魅力 –含水高圧鉱物・含水アルミノケイ酸塩ガラスを例に–

Microscopic Description of the Polyamorphic Phases of Triphenyl Phosphite by Means of Multidimensional Solid-State NMR Spectroscopy

The structural properties of a second, apparently amorphous phase (aII) of the molecular glass former triphenyl phosphite were studied by means of multidimensional solid-state NMR spectroscopy and X-ray diffraction. Phase aII was prepared by annealing the supercooled liquid in the temperature range 210 K <or= T(a) <or= 230 K. In addition to 1D (1)H and (31)P spectra and spin-lattice relaxation data, we used (31)P radio-frequency-driven spin-diffusion exchange spectroscopy to analyze the arrangement of neighboring TPP molecules on both a local and intermediate scale. For the first time, our results give a detailed microscopic description of phase aII. For T(a) > 223 K a nano- or microcrystalline material is formed, whereas for T(a) < 223 K phase aII is homogeneous and disordered. Our data strongly suggest that some of the TPP molecules in phase aII tend toward a parallel alignment. The regions, where the molecules preferentially align appear to be spatially separated and consist of only a few molecules. Whereas the mean cubic expansion of an individual region does not change within the experimental error, the percentage of correlated molecules increases with rising T(a). Based on our results, phase aII can consistently be described as a second liquid, where a part of the molecules exhibit structural correlations. The transformation of the supercooled liquid into phase aII is therefore considered as a liquid-liquid phase transition.

Resolution enhancement in multidimensional solid-state NMR spectroscopy of proteins using spin-state selection.

We show that the resolution of homonuclear multidimensional solid-state NMR correlation experiments can be significantly improved using transition selection and spin-state-selective polarization transfer techniques. The selection and transfer of single states allow the removal of the J-coupling contribution from the line width in both the direct and indirect spectral dimensions. This is demonstrated with a new spin-state-selective CO-Calpha correlation experiment, applied to a microcrystalline 85-residue protein. With this new sequence, all four components of the CO-Calpha cross-peaks are separated into different spectra, obtained by linear combination of four recorded data sets. Line narrowing of up to 44% was obtained on the protein sample for the spin-state-selective CO-Calpha spectrum compared to a standard spin-diffusion experiment. The new technique also allows an easy distinction between "direct" and "relayed" transfer cross-peaks.