Nuclear Magnetic Resonance Spectroscopy Experiments Research Articles

Fluorine Labeling and 19F NMR Spectroscopy to Study Biological Molecules and Molecular Complexes.

High-resolution nuclear magnetic resonance (NMR) spectroscopy represents a key methodology for studying biomolecules and their interplay with other molecules. Recent developments in labeling strategies have made it possible to incorporate fluorine into proteins and peptides reliably, with manageable efforts and, importantly, in a highly site-specific manner. Paired with its excellent NMR spectroscopic properties and absence in most biological systems, fluorine has enabled scientists to investigate a rather wide range of scientific objectives, including protein folding, protein dynamics and drug discovery. Furthermore, NMR spectroscopic experiments can be conducted in complex environments, such as cell lysate or directly inside living cells. This review presents selected studies demonstrating how 19F NMR spectroscopic approaches enable to contribute to the understanding of biomolecular processes. Thereby the focus has been set to labeling strategies available and specific NMR experiments performed to answer the underlying scientific objective.

Isolation and Characterization of Stigmasterol from Psidium guajava Leaves: A Promising Bioactive Compound with Therapeutic Potential

This study aimed to isolate and characterize bioactive compounds from the leaves of Psidium guajava Linn. The hydroethanolic extract yielded 32% (80 g) from the crude material, which was subjected to column chromatography for fractionation. Structural elucidation of the isolated compound was performed using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy, including COSY, HSQC, and HMBC experiments. The spectral data confirmed the presence of stigmasterol, characterized by its distinct chemical shifts and long-range correlations between carbon and proton atoms. Stigmasterol was isolated as a white, crystalline solid and identified by its unique physio-chemical properties, such as solubility in organic solvents, a melting point of 163-164°C, and molecular formula C29H48O. This compound is known for its significant biological activities, including antibacterial, antimalarial, anti-inflammatory, antioxidant, and anticancer effects. By employing advanced techniques like 1D and 2D NMR spectroscopy, the study provides precise structural elucidation of stigmasterol, contributing to natural product research and reinforcing the medicinal potential of guava leaves as a source of pharmacologically active compounds. This adds to the existing knowledge of the plant’s bioactive components and their applications in medicinal chemistry

Oxidative stress-induced degradation of Brinzolamide: Isolation and in-depth characterization of unique hydroxylamine and oxime degradation products

Since the safety and efficacy of therapeutic products are strongly related to their stability and purity, impurities including the unavoidable degradation products may affect the pharmacological effect. The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines Q3A requires the identification of process impurities and as well as degradation products in any drug substance to assess the inherent stability of the drug. The present work involves an ICH-guided degradation study for the Brinzolamide (BRZ), a topical ophthalmic drug which is generally used to lower the intraocular pressure (IOP) during glaucoma. Under oxidative stress at room temperature for 20 h, four degradation products (namely BRZ-Pk1, BRZ-PK2, BRZ-Pk3, and BRZ-Pk4) are isolated using advanced chromatographic techniques. Upon confirming the masses of the compounds using High-resolution mass spectrometry (HRMS), functional groups are identified with the help of Fourier-transform infrared spectroscopy (FT-IR). Extensive 1-dimensional (1D) and 2-dimensional (2D) Nuclear Magnetic Resonance spectroscopic (NMR) experiments especially 1D nOe, 1H-13C-HSQC and 1H-13C-HMBC unequivocally confirm the structures. Among the four compounds analyzed, three (BRZ-Pk1, BRZ-Pk2, and BRZ-Pk4) are novel, while BRZ-Pk3 was previously reported solely with mass spectrometric data. Nitrogen-based 2D NMR experiments are crucial for determining the oxidation state of hydroxylamine and oxime products within the molecules, and 1D nOe measurements help confirming E/Z isomerism (geometrical isomerism) for BRZ-Pk2 and BRZ-Pk4. All the proposed structures are justified with appropriate analytical data. The proposed mechanisms are expected to help in identifying the possible degradation pathways for similar pharmaceutical candidates.

Peptides as modulators of FPPS enzyme: A multifaceted evaluation from the design to the mechanism of action

Bone diseases are medical conditions caused by the loss of bone homeostasis consecutive to increased osteoclast activity and diminished osteoblast activity. The mevalonate pathway (MVA) is crucial for maintaining this balance since it drives the post-translational prenylation of small guanosine triphosphatases (GTPases) proteins. Farnesyl pyrophosphate synthase (FPPS) plays a crucial role in the MVA pathway. Consequently, in the treatment of bone-related diseases, FPPS is the target of FDA-approved nitrogen-containing bisphosphonates (N-BPs), which have tropism mainly for bone tissue due to their poor penetration in soft tissues. The development of inhibitors targeting the FPPS enzyme has garnered significant interest in recent decades due to FPPS's role in the biosynthesis of cholesterol and other isoprenoids, which are implicated in cancer, bone diseases, and other conditions. In this study, we describe a multidisciplinary approach to designing novel FPPS inhibitors, combining computational modeling, biochemical assays, and biophysical techniques. A series of peptides and phosphopeptides were designed, synthesized, and evaluated for their ability to inhibit FPPS activity. Molecular docking was employed to predict the binding modes of these compounds to FPPS, while Surface Plasmon Resonance (SPR) and Nuclear Magnetic Resonance (NMR) spectroscopy experiments – based on Saturation Transfer Difference (STD) and an enzymatic NMR assay – were used to measure their binding affinities and kinetics. The biological activity of the most promising compounds was further assessed in cellular assays using murine colorectal cancer (CRC) cells. Additionally, genomics and metabolomics profiling allowed to unravel the possible mechanisms underlying the activity of the peptides, confirming their involvement in the modulation of the MVA pathway. Our findings demonstrate that the designed peptides and phosphopeptides exhibit significant inhibitory activity against FPPS and possess antiproliferative effects on CRC cells, suggesting their potential as therapeutic agents for cancer.

The Persistence of Hydrogen Bonds in Pyrimidinones: From Solution to Crystal.

Pyrimidinone scaffolds are present in a wide array of molecules with synthetic and pharmacological utility. The inherent properties of these compounds may be attributed to intermolecular interactions analogous to the interactions that molecules tend to establish with active sites. Pyrimidinones and their fused derivatives have garnered significant interest due to their structural features, which resemble nitrogenous bases, the foundational building blocks of DNA and RNA. Similarly, pyrimidinones are predisposed to forming N-H···O hydrogen bonds akin to nitrogenous bases. Given this context, this study explored the supramolecular features and the predisposition to form hydrogen bonds in a series of 18 substituted 4-(trihalomethyl)-2(1H)-pyrimidinones. The formation of hydrogen bonds was observed in solution via nuclear magnetic resonance (NMR) spectroscopy experiments, and subsequently confirmed in the crystalline solid state. Hence, the 18 compounds were crystallized through crystallization assays by slow solvent evaporation, followed by single-crystal X-ray diffraction (SC-XRD). The supramolecular cluster demarcation was employed to evaluate all intermolecular interactions, and all crystalline structures exhibited robust hydrogen bonds, with an average energy of approximately -21.64 kcal mol-1 (∼19% of the total stabilization energy of the supramolecular clusters), irrespective of the substituents at positions 4, 5, or 6 of the pyrimidinone core. To elucidate the nature of these hydrogen bonds, an analysis based on the quantum theory of atoms in molecules (QTAIM) revealed that the predominant intermolecular interactions are N-H···O (average of -16.55 kcal mol-1) and C-H···O (average of -6.48 kcal mol-1). Through proposing crystallization mechanisms based on molecular stabilization energy data and contact areas between molecules and employing the supramolecular cluster and retrocrystallization concepts, it was determined that altering the halogen (F/Cl) at position 4 of the pyrimidinone nucleus modifies the crystallization mechanism pathway. Notably, the hydrogen bonds present in the initial proposed steps were confirmed by 1H NMR experiments using concentration-dependent techniques.

Thermal and spectroscopic (IR, NMR) studies of bulk ammonia borane – Polyethylene oxide composites: A potential hydrogen storage system

We utilized differential scanning calorimeter (DSC), Fourier-transformed infrared spectroscopy (FT-IR), and solid-state nuclear magnetic resonance spectroscopy (NMR) techniques to understand the dehydrogenation mechanism of ammonia borane (AB) and its polymer composites. The results indicated that the polymeric composites with higher polyethylene oxide (PEO) mass ratio involve the possible breakdown of dative bond and the formation of new interaction (H-bonding) between the AB and the polymer. The activation energies were calculated in the temperature range of 25 °C and 300 °C which were found to be lower than the pristine AB. 15N and 11B NMR studies at room temperature showed evidence for a possible interaction, H-bonding, between AB and PEO. The NMR experiments at 85 °C were conducted to investigate the isothermal decomposition during several hours. Results indicated that the pristine AB takes longer incubation time, however the polymeric composite readily decomposes at 85 °C. Both showed proof for the formation of byproducts. Moreover, IR study showed evidence to support the interaction between AB and PEO.

Mechanistic and Structural Insights on Difluoromethyl-1,3,4-oxadiazole Inhibitors of HDAC6.

Histone deacetylase 6 (HDAC6) is increasingly recognized for its potential in targeted disease therapy. This study delves into the mechanistic and structural nuances of HDAC6 inhibition by difluoromethyl-1,3,4-oxadiazole (DFMO) derivatives, a class of non-hydroxamic inhibitors with remarkable selectivity and potency. Employing a combination of nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) kinetic experiments, comprehensive enzymatic characterizations, and X-ray crystallography, we dissect the intricate details of the DFMO-HDAC6 interaction dynamics. More specifically, we find that the chemical structure of a DMFO and the binding mode of its difluoroacetylhydrazide derivative are crucial in determining the predominant hydrolysis mechanism. Our findings provide additional insights into two different mechanisms of DFMO hydrolysis, thus contributing to a better understanding of the HDAC6 inhibition by oxadiazoles in disease modulation and therapeutic intervention.

ABC block copolymer micelles driving the thermogelation: Scattering, imaging and spectroscopy

Thermoresponsive polymers have attracted much scientific attention due to their capacity for temperature-driven hydrogel formation. For biomedical applications, such as drug delivery, this transition should be tuned below body temperature to facilitate controlled and targeted drug release. We have recently developed a thermoresponsive polymer that forms gel at low concentrations (2 w/w%) in aqueous media and offers a cost-effective alternative to thermoresponsive systems currently being applied in clinics. This polymer is an ABC triblock terpolymer, where A, B, and C correspond to oligo(ethylene glycol) methyl ether methacrylate with average Mn 300 g mol−1 (OEGMA300), n-butyl methacrylate (BuMA), and di(ethylene glycol) methyl ether methacrylate (DEGMA). To investigate the self-assembly and the gelation mechanism in diluted solutions, we used small-angle neutron scattering (SANS) on 1 w/w% (below the gelation concentration) and 5 w/w% solutions (above the gelation concentration). As a comparison, we also investigated the solutions of the most studied thermoresponsive polymer, namely, Pluronic F127, an ABA triblock bipolymer made of ethylene glycol (A) and propylene glycol (B) blocks. SANS revealed that the in-house synthesised polymer forms elliptical cylinders, whose length increases significantly with temperature. In contrast, Pluronic F127 solutions form core-shell spherical micelles, which slightly elongate with temperature. Transmission electron microscopy images support the SANS findings, with tubular/worm structures being present. Variable-temperature circular dichroism (CD) and proton nuclear magnetic resonance (1H NMR) spectroscopy experiments reveal insights on the tacticity, structural changes, and molecular origin of the self-assembly.

Chemical composition of soil humin in an organic soil profile

Humin is identified as the most recalcitrant fraction of soil organic matter, but its synthesis and depth variability in the soil profile are unknown. Here, we suggest that carboxyl-rich alicyclic structures (CRAM) and fused aromatic ring structures (FAR) can process significant components of the humin structure. We conducted molecular-level characterization of humin using advanced solid-state nuclear magnetic resonance spectroscopy (SSNMR) experiments and calculated the proportion of FAR and functionalities of CRAM (OCq, –C(CH)n, –CH3) structures. Dipolar dephased (dd) direct polarization magic angle spinning (DPMAS) NMR experiments provided insights into non-protonated carbon and mobile quaternary carbons. We calculated the proportions of non-protonated aromatic carbon and non-polar aliphatic C in the organic layers of the topsoil (Oa), mid-soil (Om), and mineral subsoil (Cg). It was evident that the total aliphatic carbon constitutes a significant proportion of humin, as is the non-protonated C attached to CH3. The 13C dd/DPMAS NMR spectrum of Cg humin clearly showed the formation and preservation of hydrophobic OCq, which is indicative of CRAM structures. CRAM structures could be attached to FAR, which makes the whole structure relatively more hydrophobic, a critical humin functionality in deeper soil. The findings from our research can be successfully utilized in terrestrial carbon sequestration studies to amplify the potential of humin as a recalcitrant carbon reservoir.

The lasting impact of formation cycling on the Li-ion kinetics between SEI and the Li-metal anode and its correlation with efficiency.

Formation cycling is a critical process aimed at improving the performance of lithium ion (Li-ion) batteries during subsequent use. Achieving highly reversible Li-metal anodes, which would boost battery energy density, is a formidable challenge. Here, formation cycling and its impact on the subsequent cycling are largely unexplored. Through solid-state nuclear magnetic resonance (ssNMR) spectroscopy experiments, we reveal the critical role of the Li-ion diffusion dynamics between the electrodeposited Li-metal (ED-Li) and the as-formed solid electrolyte interphase (SEI). The most stable cycling performance is realized after formation cycling at a relatively high current density, causing an optimum in Li-ion diffusion over the Li-metal-SEI interface. We can relate this to a specific balance in the SEI chemistry, explaining the lasting impact of formation cycling. Thereby, this work highlights the importance and opportunities of regulating initial electrochemical conditions for improving the stability and life cycle of lithium metal batteries.

1H and 13C chemical shift-structure effects in anhydrous β-caffeine and four caffeine-diacid cocrystals probed by solid-state NMR experiments and DFT calculations.

By using density functional theory (DFT) calculations, we refined the H atom positions in the structures of β-caffeine (C), α-oxalic acid (OA; (COOH)2), α-(COOH)2·2H2O, β-malonic acid (MA), β-glutaric acid (GA), and I-maleic acid (ME), along with their corresponding cocrystals of 2 : 1 (2C-OA, 2C-MA) or 1 : 1 (C-GA, C-ME) stoichiometry. The corresponding 13C/1H chemical shifts obtained by gauge including projector augmented wave (GIPAW) calculations agreed overall very well with results from magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy experiments. Chemical-shift/structure trends of the precursors and cocrystals were examined, where good linear correlations resulted for all COO1H sites against the H⋯O and/or H⋯N H-bond distance, whereas a general correlation was neither found for the aliphatic/caffeine-stemming 1H sites nor any 13C chemical shift against either the intermolecular hydrogen- or tetrel-bond distance, except for the 13COOH sites of the 2C-OA, 2C-MA, and C-GA cocrystals, which are involved in a strong COOH⋯N bond with caffeine that is responsible for the main supramolecular stabilization of the cocrystal. We provide the first complete 13C NMR spectral assignment of the structurally disordered anhydrous β-caffeine polymorph. The results are discussed in relation to previous literature on the disordered α-caffeine polymorph and the ordered hydrated counterpart, along with recommendations for NMR experimentation that will secure sufficient 13C signal-resolution for reliable resonance/site assignments.

Synergistic dopa-reinforced fluid hydrosol as highly efficient coal dust suppressant

A highly efficient coal dust suppressant with low initial viscosity and high adhesion-solidification properties was fabricated by reinforcing a polyacrylic acid hydrosol with dopa and glutathione (DG) redox system. The synthesis mechanism and dust suppression properties of the dust suppressant were investigated by ultraviolet–visible spectroscopy, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy experiments combined with density functional theory calculations. The polyacrylic acid hydrosol was synthesized by free radical polymerization with an optimal concentration ratio of 0.36 % ammonium persulfate to 9 % acrylic acid; the DG redox system presented a catechol-quinone dynamic equilibrium, and the dopa polymer reinforcing adhesion was synthesized by the reverse dismutation and polymerization of dopa and dopaquinone. Results revealed that the dust suppressant system formed a multiple hydrogen bonding cross-linking network, dominated by strong double hydrogen bonding interaction formed between the carboxyl groups of dopa polymer and polyacrylic acid, and synergized by hydrogen bonds between the carboxyl groups of glutathione and PAA, and between the hydroxyl and carboxyl groups of dopa and dopaquinone. Moreover, the − OH and − COOH groups in the dust suppressant system were more tightly bonded after dehydration and can form a mesh film to effectively adhere and solidify coal dust, and the coal crust film did not raise dust at 20.526 ± 0.083 m/s wind speed.

Diamine-appended metal-organic framework for carbon capture from wet flue gas: Characteristics and mechanism

Due to the superior CO2 adsorption capacity and selectivity, amine-functional solid adsorbents have received increasing attention. Nevertheless, amine-functionalized polyporous materials have a large performance deviation when considering carbon removal capacity under wet flue gas. Therefore, a variety of metal–organic frameworks (MOFs) with amine functionality are synthesized in this work by appending diamine with a propylene linker to Mg2(dobpdc) (dobpdc4- = 4,4′-dioxido-3,3′-biphenyldicarboxylate) and screened under the simulated flue gas environment with a high water content (7 v%). The results indicate that ndmpn-grafted Mg2(dobpdc) (ndmpn = N,N-dimethyl-1,3-propanediamine) has a high CO2 adsorption capacity of 1.72 mmol/g at 60 °C with an extremely low regeneration heat (2.26 GJ/ton CO2 at the desorption temperature of 145 °C). Adsorption property of ndmpn-Mg2(dobpdc) at high humidity is even more excellent than that of another well-reported diaminopropene-appended MOF, dmpn-Mg2(dobpdc) (dmpn = 2,2-dimethyl-1,3-propanediamine). Herein, van der Waals (vdW)-corrected density functional theory (DFT) calculations are used to quantitatively analyze binding strengths and water effects on it between diamine-appended Mg2(dobpdc) and CO2. It is revealed that the addition of water makes ammonium carbamate chains produced in ndmpn-Mg2(dobpdc) more stable. These chemisorption structures under humid conditions have also been disclosed by using 15N solid-state nuclear magnetic resonance (NMR) spectroscopy experiments and DFT calculation. To conclude, we unveil the binary adsorption characteristics and mechanism of ndmpn-Mg2(dobpdc). It enables a thorough understanding of this compound and highlights its potential as a promising adsorbent under humid conditions for post-combustion applications.

Small-Molecule Inhibition of KRAS through Conformational Selection.

Mutations in KRAS account for about 20% of human cancers. Despite the major progress in recent years toward the development of KRAS inhibitors, including the discovery of covalent inhibitors of the G12C KRAS variant for the treatment of non-small-cell lung cancer, much work remains to be done to discover broad-acting inhibitors to treat many other KRAS-driven cancers. In a previous report, we showed that a 308.4 Da small-molecule ligand [(2R)-2-(N'-(1H-indole-3-carbonyl)hydrazino)-2-phenyl-acetamide] binds to KRAS with low micro-molar affinity [Chem. Biol. Drug Des.2019; 94(2):1441-1456]. Binding of this ligand, which we call ACA22, to the p1 pocket of KRAS and its interactions with residues at beta-strand 1 and the switch loops have been supported by data from nuclear magnetic resonance spectroscopy and microscale thermophoresis experiments. However, the inhibitory potential of the compound was not demonstrated. Here, we show that ACA22 inhibits KRAS-mediated signal transduction in cells expressing wild type (WT) and G12D mutant KRAS and reduces levels of guanosine triphosphate-loaded WT KRAS more effectively than G12D KRAS. We ruled out the direct effect on nucleotide exchange or effector binding as possible mechanisms of inhibition using a variety of biophysical assays. Combining these observations with binding data that show comparable affinities of the compound for the active and inactive forms of the mutant but not the WT, we propose conformational selection as a possible mechanism of action of ACA22.

Cardiometabolic disease risk markers are increased following burn injury in children.

Burn injury in children causes prolonged systemic effects on physiology and metabolism leading to increased morbidity and mortality, yet much remains undefined regarding the metabolic trajectory towards specific health outcomes. A multi-platform strategy was implemented to evaluate the long-term immuno-metabolic consequences of burn injury combining metabolite, lipoprotein, and cytokine panels. Plasma samples from 36 children aged 4-8 years were collected 3 years after a burn injury together with 21 samples from non-injured age and sex matched controls. Three different 1H Nuclear Magnetic Resonance spectroscopic experiments were applied to capture information on plasma low molecular weight metabolites, lipoproteins, and α-1-acid glycoprotein. Burn injury was characterized by underlying signatures of hyperglycaemia, hypermetabolism and inflammation, suggesting disruption of multiple pathways relating to glycolysis, tricarboxylic acid cycle, amino acid metabolism and the urea cycle. In addition, very low-density lipoprotein sub-components were significantly reduced in participants with burn injury whereas small-dense low density lipoprotein particles were significantly elevated in the burn injured patient plasma compared to uninjured controls, potentially indicative of modified cardiometabolic risk after a burn. Weighted-node Metabolite Correlation Network Analysis was restricted to the significantly differential features (q <0.05) between the children with and without burn injury and demonstrated a striking disparity in the number of statistical correlations between cytokines, lipoproteins, and small molecular metabolites in the injured groups, with increased correlations between these groups. These findings suggest a 'metabolic memory' of burn defined by a signature of interlinked and perturbed immune and metabolic function. Burn injury is associated with a series of adverse metabolic changes that persist chronically and are independent of burn severity and this study demonstrates increased risk of cardiovascular disease in the long-term. These findings highlight a crucial need for improved longer term monitoring of cardiometabolic health in a vulnerable population of children that have undergone burn injury.

NMR proven albumin interaction with metabolites in complex mixtures

One critical step in new drugs development is the investigation of the interactions between drug candidate and target protein. Nuclear Magnetic Resonance Spectroscopy (NMR) is a well-established technique for studding these interactions. Due to its availability and structural similarities to human albumin, bovine serum albumin (BSA) is widely accepted as a model for investigating the binding of small molecules to serum albumin. We report here on the evaluation of binding interactions between BSA and 18 metabolites using saturation transfer difference (STD) NMR experiments. Positive STD signals that indicate metabolite-protein interactions were obtained for leucine, pyruvic acid, valine, threonine, alanine, 4-aminohippuric acid and tryptophan.

Molecular Assessment of Metabolome Alterations in Lotus japonicus Roots Induced by Arbuscular Mycorrhiza

AbstractAn arbuscular mycorrhiza symbiosis, which is established by 80% of all vascular plants and Glomeromycota fungi, can boost the growth, stress tolerance, and yield of agricultural crop plants by increasing the mineral supply of the host plant [1]. Mineral nutrients absorbed by the fungus are exchanged for photoassimilates from the plant via highly branched fungal structures called arbuscules which are formed within root cortex cells [2]. The process of arbuscule formation and degradation is highly dynamic and accompanied by considerable cell reprogramming [3], but there is only limited knowledge on the influence of arbuscular mycorrhiza on the host metabolome.We investigated alterations of the host plant's root metabolome induced by arbuscular mycorrhizal symbiosis using the model legume Lotus japonicus. Methanol extracts of mycorrhizal (myc) and non‐mycorrhizal roots (mock) were analyzed employing ultra‐highperformance liquid chromatography–electrospray ionization–time‐of‐flight–ion mobility–mass spectrometry (UPLC–ESI–ToF–IM–MS) in an untargeted metabolomics approach. Up‐regulated marker metabolites were identified via principal components analysis (PCA) and orthogonal partial least squares–discriminant analysis (OPLS–DA) depicted as S‐plots, and their structures elucidated by co‐chromatography with authentic standards or by isolation from L. japonicus roots using preparative HPLC and one‐ and two‐dimensional nuclear magnetic resonance spectroscopy (NMR) experiments. We isolated three previously unknown mycorrhizal marker polyphenols from L. japonicus roots, one being a coumaronochromone, one pterocarp‐6a‐ene, and one aryl benzofuran carboxaldehyde. Additionally, we identified three more coumaronochromones, three flavonoids, three isoflavonoids, and one coumestan in mycorrhized L. japonicus.

Understanding cooperativity effects in RNA structure probing experiments.

Small molecule chemical probes, which form covalent bonds with atoms of flexible nucleotides, are commonly used to gain insight into the structure adopted by an RNA. In this work, we use selective 2’ hydroxyl acylation analyzed by primer extension (SHAPE) and nuclear magnetic resonance (NMR) spectroscopy experiments to explore whether the structure of an RNA is modulated by chemical probe binding events. We find that as the concentration of a chemical probe increases, modified nucleotides locally modulate the RNA structure, resulting in the increase or decrease of SHAPE reactivity in surrounding nucleotides. This cooperative effect is dependent on both chemical probe concentration and size. Critically, this effect impacts the accuracy of predicted RNA secondary structures when guided by chemical probing experiments. Altogether, our work highlights the importance of optimizing the conditions of chemical probing experiments to obtain secondary structural information about an RNA.

Optimization of Diffusion-Ordered NMR Spectroscopy Experiments for High-Throughput Automation in Human Metabolic Phenotyping.

The diffusion-ordered nuclear magnetic resonance spectroscopy (DOSY) experiment allows the calculation of diffusion coefficient values of metabolites in complex mixtures. However, this experiment has not yet been broadly used for metabolic profiling due to lack of a standardized protocol. Here we propose a pipeline for the DOSY experimental setup and data processing in metabolic phenotyping studies. Due to the complexity of biological samples, three experiments (a standard DOSY, a relaxation-edited DOSY, and a diffusion-edited DOSY) have been optimized to provide DOSY metabolic profiles with peak-picked diffusion coefficients for over 90% of signals visible in the one-dimensional 1H general biofluid profile in as little as 3 min 36 s. The developed parameter sets and tools are straightforward to implement and can facilitate the use of DOSY for metabolic profiling of human blood plasma and urine samples.

Monitoring the Solution Persistence of Porous Coordination Cages with Diffusion NMR Spectroscopy and Cryogenic Transmission Electron Microscopy

As a unique class of molecular adsorbents, porous coordination cages (PCCs) have garnered interest because of their potential solubility, which enables applications not available to activated carbons, zeolites, metal–organic frameworks (MOFs), and covalent organic frameworks (COFs), such as covalent membrane incorporation, solution-based ion binding, and facile incorporation into porous liquids. The identification of key aspects of cage behavior in solution such as the self-assembly process, structural integrity in solution, conformational changes, and cage interactions with guest molecules is necessary to broaden the utility of soluble porous cages. Many characterization strategies for permanently porous coordination cages have been limited to the solid state and have relied heavily on X-ray diffraction, electron microscopy, and infrared (IR), UV–vis, and nuclear magnetic resonance (NMR) spectroscopies. As such, definitive evidence of cage behavior while in solution has been lacking, as the often-paramagnetic nature of permanently porous coordination cages complicates one-dimensional NMR spectroscopy experiments. Here, we explore the combined use of diffusion-ordered spectroscopy NMR (DOSY NMR), transmission electron microscopy (TEM), and cryogenic transmission electron microscopy (cryo-TEM) to confirm the persistence of soluble PCCs in various solutions.