Electron and Spin Delocalization in [Co6 Se8 (PEt3 )6 ]0/+1 Superatoms

Molecular clusters can function as nanoscale atoms/superatoms, assembling into superatomic solids, a new class of solid-state materials with designable properties through modifications on superatoms. To explore possibilities on diversifying building blocks, here we thoroughly studied one representative superatom, Co6 Se8 (PEt3 )6 . We probed its structural, electronic, and magnetic properties and revealed its detailed electronic structure as valence electrons delocalize over inorganic [Co6 Se8 ] core while ligands function as an insulated shell. 59 Co SSNMR measurements on the core and 31 P, 13 C on the ligands show that the neutral Co6 Se8 (PEt3 )6 is diamagnetic and symmetric, with all ligands magnetically equivalent. Quantum computations cross-validate NMR results and reveal degenerate delocalized HOMO orbitals, indicating aromaticity. Ligand substitution keeps the inorganic core nearly intact. After losing one electron, the unpaired electron in [Co6 Se8 (PEt3 )6 ]+1 is delocalized, causing paramagnetism and a delocalized electron spin. Notably, this feature of electron/spin delocalization over a large cluster is attractive for special single-electron devices.

3D to 0D cesium lead bromide: A 79/81Br NMR, NQR and theoretical investigation

Inorganic metal halides offer unprecedented tunability through elemental variation of simple three-element compositions, but can exhibit complicated phase behaviour, degradation, and microscopic phenomena (disorder/dynamics) that play an integral role for the bulk-level chemical and physical properties of these materials. Understanding the halogen chemical environment in such materials is crucial to addressing many of the concerns regarding implementing these materials in commercial applications. In this study, a combined solid-state nuclear magnetic resonance, nuclear quadrupole resonance and quantum chemical computation approach is used to interrogate the Br chemical environment in a series of related inorganic lead bromide materials: CsPbBr₃, CsPb₂Br₅, and Cs₄PbBr₆. The quadrupole coupling constants (C_Q) were determined to range from 61 to 114 MHz for ⁸¹Br, with CsPbBr₃ exhibiting the largest measured C_Q and Cs₄PbBr₆ the smallest. GIPAW DFT was shown to be an excellent pre-screening tool for estimating the EFG of Br materials and can increase experimental efficiency by providing good starting estimates for acquisition. Finally, the combination of theory and experiment to inform the best methods for expanding further to the other quadrupolar halogens is discussed.

Corrigendum: Calcium interactions in amelogenin-derived peptide assembly

[This corrects the article DOI: 10.3389/fphys.2022.1063970.].

Calcium interactions in amelogenin-derived peptide assembly

Phosphorylation of serine residues has been recognized as a pivotal event in the evolution of mineralized tissues in many biological systems. During enamel development, the extracellular matrix protein amelogenin is most abundant and appears to be critical to the extreme high aspect ratios (length:width) of apatite mineral fibers reaching several millimeters in larger mammalian teeth. A 14-residue peptide (14P2, residues Gly8 to Thr21) was previously identified as a key sequence mediating amelogenin assembly formation, the domain also contains the native single phosphoserine residue (Ser16) of the full-length amelogenin. In this research, 14P2 and its phosphorylated form (p14P2) were investigated at pH 6.0 with various calcium and phosphate ion concentrations, indicating that both peptides could self-assemble into amyloid-like conformation but with differences in structural details. With calcium, the distance between ³¹P within the p14P2 self-assemblies is averaged to be 4.4 ± 0.2Å, determined by solid-state NMR ³¹P PITHIRDS-CT experiments. Combining with other experimental results, solid-state Nuclear Magnetic Resonance (SSNMR) suggests that the p14P2 self-assemblies are in parallel in-register β-sheet conformation and divalent calcium ions most likely connect two adjacent peptide chains by binding to the phosphate group of Ser16 and the carboxylate of Glu18 side-chain. This study on the interactions between calcium ions and amelogenin-derived peptides provides insights on how amelogenin may self-assemble in the presence of calcium ions in early enamel development.

Spectroscopic signatures of bilayer ordering in native biological membranes

Membrane proteins and polycyclic lipids like cholesterol and hopanoids coordinate phospholipid bilayer ordering. This phenomenon manifests as partitioning of the liquid crystalline phase into liquid-ordered (Lo) and liquid-disordered (Ld) regions. In Eukaryotes, microdomains are rich in cholesterol and sphingolipids and serve as signal transduction scaffolds. In Prokaryotes, Lo microdomains increase pathogenicity and antimicrobial resistance. Previously, we identified spectroscopically distinct chemical shift signatures for all-trans (AT) and trans-gauche (TG) acyl chain conformations, cyclopropyl ring lipids (CPR), and hopanoids in prokaryotic lipid extracts and used Polarization Transfer (PT) SSNMR to investigate bilayer ordering. To investigate how these findings relate to native bilayer organization, we interrogate whole cell and whole membrane extract samples of Burkholderia thailendensis to investigate bilayer ordering in situ. In 13C-13C 2D SSNMR spectra, we assigned chemical shifts for lipid species in both samples, showing conservation of lipids of interest in our native membrane sample. A one-dimensional temperature series of PT SSNMR and transverse relaxation measurements of AT versus TG acyl conformations in the membrane sample confirm bilayer ordering and a broadened phase transition centered at a lower-than-expected temperature. Bulk protein backbone Cα dynamics and correlations consistent with lipid-protein contacts within are further indicative of microdomain formation and lipid ordering. In aggregate, these findings provide evidence for microdomain formation in vivo and provide insight into phase separation and transition mechanics in biological membranes.

Separated quadrupole and shift interactions of 2H NMR spectra in paramagnetic solids by asymmetric pulse sequences

Separated pure-quadrupole (PQ) and -shift (PS) spectra of ²H nuclear magnetic resonance (NMR) of paramagnetic solids are obtained and correlated by simple pulse sequences that can acquire the full magnetization under ideal conditions. Two-dimensional NMR signals obtained using an asymmetric π-pulse-inserted quadrupole-echo (APIQE) sequence yielded separated spectra through the skew operation of an affine transform (AT) before a Fourier transform. Modified APIQE sequences that acquire whole echo signals were fabricated, and separated PQ and PS spectra were obtained by applying a combination of AT, such as rotation and skew operations, to the signal data. These methods were demonstrated for diamagnetic Zn(CD₃CO₂)₂⋅2H₂O and paramagnetic Nd(CD₃CO₂)₃⋅1.5H₂O. Further, the dynamics of the D₂O molecule and [Co(D₂O)₆]²⁺ ion in paramagnetic CoSiF₆⋅6D₂O was analyzed based on the temperature dependence of the separated spectra.

A structural analysis of 2,5-diaryl-4H-2,4-dihydro-3H-1,2,4-triazol-3-ones: NMR in the solid state, X-ray crystallography, and GIPAW calculations

The ¹ H, ¹³ C, ¹⁵ N, and ¹⁹ F nuclear magnetic resonance (NMR) spectra of 11 2,5-diaryl-2,4-dihydro-3H-1,2,4-triazol-3-ones have been acquired in DMSO-d₆ solution and the ¹³ C, ¹⁵ N, and ¹⁹ F NMR spectra have also been acquired in the solid state (solid-state nuclear magnetic resonance [SSNMR] and magic angle spinning [MAS]). The X-ray structures of Compounds 3, 5, and 6 have been determined by X-ray diffraction. Theoretical calculations at the gauge-independent atomic orbital (GIAO)/B3LYP/6-311++G(d,p) level have provided a set of 321 chemical shifts that were compared with 310 experimental values in DMSO-d₆ . To obtain good agreements, some effects need to be included. The SSNMR chemical shifts have been compared with gauge-including projector-augmented wave (GIPAW) calculations and with the heavy atom-light atom (HALA) effects.

Determining the degree of acetylation of chitin/chitosan using a SSNMR 13C method on the basis of cross polarization reciprocity relation

The degree of acetylation (DA) is an essential parameter for chitin and its derivatives, which determines the chemical and physical properties of the polymers. As a consequene, fast and accurate technique to determine DA is widely required when developing the relating materials. Herein, an improved quantitative SSNMR method of rQCP_Z^RC, based on the cross polarization reciprocity relation, was discussed and employed for DA testing. Three chitin/chitosan samples were chosen to evaluate the performance of rQCP_Z^RC. In comparison with quantitative DP and optimized contact time CP methods, rQCP_Z^RC is revealed as an accurate and reliable DA testing method with relative percentage errors of less than 5%. Moreover, the experimental time of rQCP_Z^RC for each sample is 5.5 h, notably shorter than DP of 36-85 h. Thus, our work suggests rQCP_Z^RC as a tool for DA testing, which is capable to accomplish with high accuracy and efficiency.

Quantification of Monomer Units in Insoluble Polymeric Active Pharmaceutical Ingredients Using Solid-State NMR Spectroscopy I: Patiromer

Although extensive precautions are taken to limit batch-to-batch variation in pharmaceutical manufacturing, differences between lots may still exist, particularly in complex formulations. When polymerization is used in the production process, the potential for varying chain lengths and incorporation of different monomers increases the likelihood of batch-to-batch variation. This poses a significant challenge for demonstrating active pharmaceutical ingredient (API) sameness between the innovator and generic drug under development. Therefore, the ability to accurately analyze and quantify the relative amounts of active ingredients present in a formulated product is critically important. Solid-state nuclear magnetic resonance (SSNMR) spectroscopy was used to identify, quantify, and compare the relative amounts of the three polymer groups in the amorphous block copolymer drug, patiromer (Veltassa^®). Techniques such as cross polarization (CP) and magic angle spinning were used to quantify each polymer group while the importance of understanding CP dynamics to obtain quantitative data was also addressed. It was found that the magnetization transfer rate and chemical shift anisotropy for different functional groups present in patiromer play a large role when optimizing parameters for spectral acquisition. Once accounted for, the average patiromer lot contained 90.9%, 7.6%, and 1.5% carboxylate, aromatic, and aliphatic blocks, respectively, with little lot-to-lot variation between different dosage strengths and expiration dates. SSNMR proved to be a sensitive analytical technique for evaluating and quantifying different monomer groups present in patiromer. This procedure may serve as a guide for similar quantitation studies on complex drug products and for demonstrating API sameness during generic drug development.

On the direct relation between REDOR and DIPSHIFT experiments in solid-state NMR

Rotational-echo double resonance (REDOR) and Dipolar-coupling chemical-shift correlation (DIPSHIFT) are commonly used experiments to probe heteronuclear dipole-dipole couplings between isolated pairs of spin-12 nuclei in magic-angle-spinning (MAS) solid-state NMR. Their widespread use is due to their robustness to experimental imperfections and a straightforward interpretation of data. Both of these experiments use rotor-synchronised π pulses to recouple the heteronuclear dipole-dipole couplings, and the observed intensity of resonances is modulated by a recoupled phase factor depending on the position or duration of the recoupling pulses. Several modifications to both of these experiments have been proposed, for example, the development of DIPSHIFT which employs strategies that mimic the multi-rotor-period nature of REDOR. We show here that REDOR and DIPSHIFT are in fact alternate implementations of the same experiment. The overt similarity in the design of REDOR and DIPSHIFT is also reflected in their theoretical description. Dipolar dephasing curves in REDOR are obtained by increasing the recoupling duration whilst keeping the position of the pulses constant, which results in a dephasing factor that is a function of only the dephasing time. DIPSHIFT, on the other hand, is a constant-time version of REDOR; the dipolar dephasing is a function of the position of the pulses with respect to the rotor period. We discuss the advantages and disadvantages of each implementation and suggest domains of applicability for these sequences.

Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques

With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’.

Spectroscopic analysis of the influence of various external factors on ethenzamide-glutaric acid (1:1) cocrystal formation

Cocrystal formation may affect manufacturability (flow, compaction and processability) as well as solubility/dissolution, hygroscopicity and stability properties of drugs. Therefore, cocrystallization could be used to improve the pharmaceutical properties of low-soluble drugs such as ethenzamide. In this project, solid-state nuclear magnetic resonance and Fourier transform infrared spectroscopy studies were performed for ethenzamide-glutaric acid to obtain more information about the ethenzamide cocrystallization process. The impact of the grinding time of the physical mixture (ethenzamide-glutaric acid) on cocrystal formation and the further spontaneous cocrystallization was evaluated using spectroscopic methods and curve-fitting analysis of the spectra. The influence of pressure on the yield of cocrystal formation was also described. Additionally, studies on the effect of magic-angle spinning during solid-state nuclear magnetic resonance spectra collection on the initiation of cocrystal formation, have been performed. Based on this research, conclusions regarding the influence of the different external factors, such as pressure during the tableting process and grinding time, on the cocrystal formation have been drawn for ethenzamide cocrystals.

The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex

The RIPK1-RIPK3 necrosome is an amyloid signaling complex that initiates TNF-induced necroptosis, serving in human immune defense, cancer, and neurodegenerative diseases. RIPK1 and RIPK3 associate through their RIP homotypic interaction motifs with consensus sequences IQIG (RIPK1) and VQVG (RIPK3). Using solid-state nuclear magnetic resonance, we determined the high-resolution structure of the RIPK1-RIPK3 core. RIPK1 and RIPK3 alternately stack (RIPK1, RIPK3, RIPK1, RIPK3, etc.) to form heterotypic β sheets. Two such β sheets bind together along a compact hydrophobic interface featuring an unusual ladder of alternating Ser (from RIPK1) and Cys (from RIPK3). The crystal structure of a four-residue RIPK3 consensus sequence is consistent with the architecture determined by NMR. The RIPK1-RIPK3 core is the first detailed structure of a hetero-amyloid and provides a potential explanation for the specificity of hetero- over homo-amyloid formation and a structural basis for understanding the mechanisms of signal transduction.

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.

Integrating High-Resolution and Solid-State Magic Angle Spinning NMR Spectroscopy and a Transcriptomic Analysis of Soybean Tissues in Response to Water Deficiency

INTRODUCTION

Solid-state NMR (SSNMR) spectroscopy methods provide chemical environment and ultrastructural details that are not easily accessible by other non-destructive, high-resolution spectral techniques. High-resolution magic angle spinning (HR-MAS) has been widely used to obtain the metabolic profile of a heterogeneous sample, combining the resolution enhancement provided by MAS in SSNMR with the shimming and locking procedures in liquid-state NMR.

OBJECTIVE

In this work, we explored the feasibility of using the HR-MAS and SSNMR techniques to identify metabolic changes in soybean leaves subjected to water-deficient conditions.

METHODOLOGY

Control and water-deficient soybean leaves were analysed using one-dimensional (1D) HR-MAS and SSNMR. Total RNA was extracted from the leaves for the transcriptomic analysis.

RESULTS

The 1 H HR-MAS and CP-MAS 13 C{1 H} spectra of soybean leaves grown with and without water deficiency stress revealed striking differences in metabolites. A total of 30 metabolites were identified, and the impact of water deficiency on the metabolite profile of soybean leaves was to induce amino acid synthesis. High expression levels of genes required for amino acid biosynthesis were highly correlated with the compounds identified by 1 H HR-MAS.

CONCLUSIONS

The integration of the 1 H HR-MAS and SSNMR spectra with the transcriptomic data provided a complete picture of the major changes in the metabolic profile of soybeans in response to water deficiency. Copyright © 2017 John Wiley & Sons, Ltd.

Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization

An experimental strategy has been developed to increase the efficiency of dynamic nuclear polarization (DNP) in solid-state NMR studies. The method makes assignments simpler, faster, and more reliable via sequential correlations of both side-chain and Cα resonances. The approach is particularly suited to complex biomolecules and systems with significant chemical-shift degeneracy. It was designed to overcome the spectral congestion and line broadening that occur due to sample freezing at the cryogenic temperatures required for DNP. Nonuniform sampling (NUS) is incorporated to achieve time-efficient collection of multidimensional data. Additionally, fast (25 kHz) magic-angle spinning (MAS) provides optimal sensitivity and resolution. Data collected in <1 wk produced a virtually complete de novo assignment of the coat protein of Pf1 virus. The peak positions and linewidths for samples near 100 K are perturbed relative to those near 273 K. These temperature-induced perturbations are strongly correlated with hydration surfaces.

Solid-state NMR and short-range order in crystalline oxides and silicates: a new tool in paramagnetic resonances

Most applications of high-resolution NMR to questions of short-range order/disorder in inorganic materials have been made in systems where ions with unpaired electron spins are of negligible concentration, with structural information extracted primarily from chemical shifts, quadrupolar coupling parameters, and nuclear dipolar couplings. In some cases, however, the often-large additional resonance shifts caused by interactions between unpaired electron and nuclear spins can provide unique new structural information in materials with contents of paramagnetic cations ranging from hundreds of ppm to several per cent and even higher. In this brief review we focus on recent work on silicate, phosphate, and oxide materials with relatively low concentrations of paramagnetic ions, where spectral resolution can remain high enough to distinguish interactions between NMR-observed nuclides and one or more magnetic neighbors in different bonding configurations in the first, second, and even farther cation shells. We illustrate the types of information available, some of the limitations of this approach, and the great prospects for future experimental and theoretical work in this field. We give examples for the effects of paramagnetic transition metal, lanthanide, and actinide cation substitutions in simple oxides, pyrochlore, zircon, monazite, olivine, garnet, pyrochlores, and olivine structures.

13C and 19F solid-state NMR and X-ray crystallographic study of halogen-bonded frameworks featuring nitrogen-containing heterocycles

Halogen bonding is a noncovalent interaction between the electrophilic region of a halogen (σ-hole) and an electron donor. We report a crystallographic and structural analysis of halogen-bonded compounds by applying a combined X-ray diffraction (XRD) and solid-state nuclear magnetic resonance (SSNMR) approach. Single-crystal XRD was first used to characterize the halogen-bonded cocrystals formed between two fluorinated halogen-bond donors (1,4-diiodotetrafluorobenzene and 1,3,5-trifluoro-2,4,6-triiodobenzene) and several nitrogen-containing heterocycles (acridine, 1,10-phenanthroline, 2,3,5,6-tetramethylpyrazine, and hexamethylenetetramine). New structures are reported for the following three cocrystals, all in the P2₁/c space group: acridine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C₆F₃I₃·C₁₃H₉N, 1,10-phenanthroline-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C₆F₃I₃·C₁₂H₈N₂, and 2,3,5,6-tetramethylpyrazine-1,3,5-trifluoro-2,4,6-triiodobenzene (1/1), C₆F₃I₃·C₈H₁₂N₂. ¹³C and ¹⁹F solid-state magic-angle spinning (MAS) NMR is shown to be a convenient method to characterize the structural features of the halogen-bond donor and acceptor, with chemical shifts attributable to cocrystal formation observed in the spectra of both nuclides. Cross polarization (CP) from ¹⁹F to ¹³C results in improved spectral sensitivity in characterizing the perfluorinated halogen-bond donor when compared to conventional ¹H CP. Gauge-including projector-augmented wave density functional theory (GIPAW DFT) calculations of magnetic shielding constants, along with optimization of the XRD structures, provide a final set of structures in best agreement with the experimental ¹³C and ¹⁹F chemical shifts. Data for carbons bonded to iodine remain outliers due to well-known relativistic effects.

Ion distribution in copper exchanged zeolites by using Si-29 spin lattice relaxation analysis

Transition metal-containing zeolites, particularly those with smaller pore size, have found extensive application in the selective catalytic reduction (SCR) of environmental pollutants containing nitrogen oxides. We report these zeolites have dramatically faster silicon-29 (Si-29) spin lattice relaxation times (T1) compared to their sodium-containing counterparts. Paramagnetic doping allows one to acquire Si-29 MAS spectra in the order of tens of seconds without significantly affecting the spectral resolution. Moreover, relaxation times depend on the method of preparation and the next-nearest neighbor silicon Qn(mAl) sites, where n=4 and m=0-4, respectively. A clear trend is noted between the effectiveness of Cu exchange and the Si-29 NMR relaxation times. It is anticipated that the availability of this tool, and the enhanced understanding of the nature of the active sites, will provide the means for designing improved SCR catalysts.

Three-dimensional structure of CAP-gly domain of mammalian dynactin determined by magic angle spinning NMR spectroscopy: conformational plasticity and interactions with end-binding protein EB1

Microtubules and their associated proteins play important roles in vesicle and organelle transport, cell motility and cell division. Perturbation of these processes by mutation typically gives rise to severe pathological conditions. In our efforts to obtain atomic information on microtubule-associated protein/microtubule interactions with the goal to understand mechanisms that might potentially assist in the development of treatments for these diseases, we have determined the three-dimensional structure of CAP-Gly (cytoskeleton-associated protein, glycine-rich) domain of mammalian dynactin by magic angle spinning NMR spectroscopy. We observe two conformations in the β2 strand encompassing residues T43-V44-A45, residues that are adjacent to the disease-associated mutation, G59S. Upon binding of CAP-Gly to microtubule plus-end tracking protein EB1, the CAP-Gly shifts to a single conformer. We find extensive chemical shift perturbations in several stretches of residues of CAP-Gly upon binding to EB1, from which we define accurately the CAP-Gly/EB1 binding interface. We also observe that the loop regions may exhibit unique flexibility, especially in the GKNDG motif, which participates in the microtubule binding. This study in conjunction with our previous reports suggests that conformational plasticity is an intrinsic property of CAP-Gly likely due to its unusually high loop content and may be required for its biological functions.