NMR Resonances Research Articles

1H, 13C and 15N resonance assignments of the first BIR domain of cellular inhibitor of apoptosis protein 1.

Cellular inhibitor of apoptosis protein-1 (cIAP-1) is member of inhibitor of apoptosis proteins (IAPs) which can affect apoptosis through interactions with caspases. cIAP-1 is a multi-domain protein and able to regulate apoptosis through interactions with proteins such as caspases and possesses E3 ligase activity. Human cIAP-1 contains three baculovirus IAP repeat (BIR) domains which are critical for protein-protein interactions. Here, we report NMR resonance assignments of the first BIR domain of human cIAP. Its secondary structures in solution were determined based on the assigned resonances. The dynamics of this domain was obtained, and our hydrogen-deuterium exchange experiment reveals that the first helix in BIR1 is exposed to the solvent. The availability of assignments of backbone and side chain resonances will be useful for probing protein-protein interactions.

Crystal structure and DNA cleavage properties of a vanadium complex [NH4][VO(O2)2(pm-im)]⋅3H2O containing 2-(1H-imidazol-2-yl)pyrimidine ligand

A new diperoxovanadium compound, [NH4][VO(O2)2(pm-im)]⋅3H2O (1) (pm-im = 2-(1H-imidazol-2-yl)pyrimidine), has been prepared from aqueous solution and its crystal structure has been determined by single-crystal X-ray diffraction. It belongs to the monoclinic P21/n space group with a = 6.798(4) Å, b = 11.468(6) Å, c = 18.073(9) Å, β = 96.020(6)°, V = 1401.3(13) Å3, and Z = 4. The asymmetric unit of 1 consists of a diperoxovanadium [VO(O2)2(pm-im)]− anion, one free NH4 + counterion, and three lattice water molecules, which are further stacked to form a three-dimensional (3D) supramolecular structure through intra- and intermolecular hydrogen bond interactions. The solution stability of the ion ([VO(O2)2(pm-im)]−) was explored using a combination of multinuclear (1H, 13C, and 51V) magnetic resonance and variable temperature NMR in a 0.15 mol L−1 NaCl/D2O solution that mimics physiological conditions. Additionally, the compound exhibits significant DNA cleavage ability under light, and the electrophoretic result shows that the super helix DNA seems to be directly cleaved into single stranded DNA.

γ-Agostic interactions in (MesCCC)Fe-Mes(L) complexes.

Agostic interactions were observed in the bound mesityl group in a series of iron compounds bearing a bis(NHC) pincer CCC ligand. The L-type ligand on [(CCC)FeIIMes(L)] complexes influences the strength of the agostic interaction and is manifested in the upfield shift of the 1H NMR resonance for the mesityl methyl resonances. The nature of the interaction was further investigated by density functional theory calculations, allowing rationalization of some unexpected trends and proving to be a powerful predictive tool.

Fluvirucins B7-B10, new antifungal macrolactams from a marine-derived Nonomuraea sp. MYH522.

Marine rare actinomycetes are an important source of secondary metabolites. From a marine-derived actinomycete Nonomuraea sp. MYH522, four new macrolactams, fluvirucins B7–B10, together with known fluvirucin B6 were isolated. Their structures were determined based on comprehensive analysis of HRESIMS and NMR spectroscopic data as well as by comparing 13C NMR resonances and optical rotation values with those for related congeners. Fluvirucins are characterized by a 14-membered macrolactam attached by an aminosugar moiety. The discovery of fluvirucins B6–B10 enriched the N-acetylated derivatives of fluvirucins. The diverse alkyl substituents at C-2 and C-6 implied substrate promiscuity in fluvirucin polyketide biosynthesis. These compounds didn't exhibit any antibacterial or antifungal activities when used alone, which suggested the importance of the free amino group in the antimicrobial activity of fluvirucins. However, fluvirucins B6, B9, and B10 showed synergistic antifungal activity with fluconazole against fluconazole-resistant isolates of Candida albicans.

Evidence for complexation-induced micro-extension of poly(vinyl alcohol) chains in interphase and amorphous domains from solid-state NMR.

The three-phase structure of poly(vinyl alcohol) (PVA)-iodine complexes was elucidated by solid-state NMR (SSNMR), of which the micro-extension of the PVA segment in the interphase and amorphous domains was directly confirmed. The three-phase structure of the PVA-iodine complex was decomposed by the inverse 13C T1-filter, where 13C NMR resonance lines of a C(H) triplet were observed in all three phases. The chain axis of ∼26% extended chains in the interphase deviates 35°-50° relative to the stretching direction, while there is only a 1° deviation for the extended chains in the crystalline domain. The increasing iodine concentration results in the increment of hydrogen-bonded C(H) fractions in both the amorphous and interphase domains, while the distribution of different C(H) fractions remains almost constant in the crystalline domain. Such an increment results from the locally extended PVA chains induced by polyiodine species (I3-/I5-), since the hydrogen bond(s) (HBs) required a specific direction. Direct evidence for this comes from the similar 13C CP/MAS spectra of C(H) in the three phases between unoriented iodine-doped PVA and highly oriented pure PVA. This supports the aggregation model for the formation mechanism of PVA-iodine complexes, where the PVA chain takes an extended zig-zag conformation.

Synthesis of benzidine-based conjugated organic materials bearing donor-acceptor groups: DFT studies and photovoltaic applications

Herein, tetraethoxymethyl, diphenyl, and dipyrenyl units have been fused with biphenyl group, via diimine bond, resulting in 3 (2 novel) benzidine derivatives 2, 4a-b. The derivatives were successfully synthesized by condensation of three different aldehydes (formaldehyde, benzaldehyde 3a, and pyrenecarboxaldehyde 3b) with benzidine in high yields. Structural identifications of the newly obtained compounds are determined by NMR, IR, UV–Vis, and HRMS spectroscopic techniques. Then, the photovoltaic properties of the organic compounds were investigated. To obtain insight into the geometric, electronic, and spectroscopic features of compounds 2, 4a-b, theoretical calculations were performed utilizing the B3LYP/6–311G(2d,2p) basis set. Theoretical 1H and 13C NMR resonance signals of compounds 2, 4a-b were estimated in the gas phase and the IEFPCM model in solvent field calculations utilizing the GIAO method at the B3LYP/6–311G(2d,2p) level and showed excellent correlation with the experimental results. A comparison of computed and experimental vibrational frequencies was performed, and significant bands were allocated. The results showed that experimental and theoretical IR frequencies had a good correlation (R2=0.9997 (2), 0.9996 (4a), and 0.9940 (4b)). To explain the relationship between the molecular structure of the compounds and photovoltaic properties, density functional theory (DFT) and its time-dependent form (TD-DFT) were utilized. The HOMO-LUMO energies and energy gap (Eg) helped understand optimal energy levels for electron absorption and transfer. The calculated band-gap of compounds 2, 4a-b were 4.705, 3.679, and 3.006 eV, respectively. The power conversion efficiency (PCE) values for the compounds 2, 4a-b were also calculated as 2.25, 2.70, and 2.80%, respectively. Compared to compounds 2 and 4a, dipyrenyl-bearing benzidine derivative 4b showed a larger redshift in the absorption wavelength with a remarkable high PCE value along with a low Eg value, which can be attributed to the greater stability of 4b due to the extended π-conjugation.Therefore, compound 4b with the d-A-π-A-D architecture is a potential candidate as useful electron transport material for DSSCs.

Detection of glucose-derived d- and l-lactate in cancer cells by the use of a chiral NMR shift reagent

BackgroundExcessive lactate production, a hallmark of cancer, is largely formed by the reduction of pyruvate via lactate dehydrogenase (LDH) to l-lactate. Although d-lactate can also be produced from glucose via the methylglyoxal pathway in small amounts, less is known about the amount of d-lactate produced in cancer cells. Since the stereoisomers of lactate cannot be distinguished by conventional 1H NMR spectroscopy, a chiral NMR shift reagent was used to fully resolve the 1H NMR resonances of d- and l-lactate.MethodsThe production of l-lactate from glucose and d-lactate from methylglyoxal was first demonstrated in freshly isolated red blood cells using the chiral NMR shift reagent, YbDO3A-trisamide. Then, two different cell lines with high GLO1 expression (H1648 and H 1395) were selected from a panel of over 80 well-characterized human NSCLC cell lines, grown to confluence in standard tissue culture media, washed with phosphate-buffered saline, and exposed to glucose in a buffer for 4 h. After 4 h, a small volume of extracellular fluid was collected and mixed with YbDO3A-trisamide for analysis by 1H NMR spectroscopy.ResultsA suspension of freshly isolated red blood cells exposed to 5mM glucose produced l-lactate as expected but very little d-lactate. To evaluate the utility of the chiral NMR shift reagent, methylglyoxal was then added to red cells along with glucose to stimulate the production of d-lactate via the glyoxalate pathway. In this case, both d-lactate and l-lactate were produced and their NMR chemical shifts assigned. NSCLC cell lines with different expression levels of GLO1 produced both l- and d-lactate after incubation with glucose and glutamine alone. A GLO1-deleted parental cell line (3553T3) showed no production of d-lactate from glucose while re-expression of GLO1 resulted in higher production of d-lactate.ConclusionsThe shift-reagent-aided NMR technique demonstrates that d-lactate is produced from glucose in NSCLC cells via the methylglyoxal pathway. The biological role of d-lactate is uncertain but a convenient method for monitoring d-lactate production could provide new insights into the biological roles of d- versus l-lactate in cancer metabolism.

Inside Cover: Background‐Free Proton NMR Spectroscopy with Radiofrequency Amplification by Stimulated Emission Radiation (Angew. Chem. Int. Ed. 50/2021)

Radiofrequency amplification by stimulated emission radiation (RASER) is the version of lasers and masers operating in the radiofrequency spectral range. In their Communication on page 26298, Eduard Y. Chekmenev and co-workers employ 61 MHz proton RASER to demonstrate robust background-free detection of biomolecular NMR resonances even in the extreme cases of fully protonated solvents and biological fluids. This approach paves the way to a wide range of high-resolution NMR and in vivo MRI applications of background-free proton detection of hyperpolarized molecules.

The trans-to-cis proline isomerization in E. coli Trx folding is accelerated by trans prolines

The conserved fold of thioredoxin (Trx)-like thiol/disulfide oxidoreductases contains an invariant cis-proline residue (P76 in Escherichia coli Trx) that is essential for Trx function and that is responsible for the folding rate-limiting step. E. coli Trx contains four additional prolines, which are all in the trans conformation in the native state. Notably, a recent study revealed that replacement of all four trans prolines in Trx by alanines (Trx variant Trx1P) further slowed the rate-limiting step 25-fold, indicating that one or several of the four trans prolines accelerate the trans-to-cis transition of P76 in Trx wild-type (wt). Here, we characterized the folding kinetics of Trx variants containing cisP76 and one or several of the natural trans prolines of Trx wt with NMR spectroscopy. First, we demonstrate that the isomerization reaction in Trx1P is a pure two-state transition between two distinct tertiary structures, in which all observed NMR resonances changes follow the same first-order kinetics. Moreover, we show that trans-P68 is the critical residue responsible for the faster folding of wt Trx relative to the single-proline (P76) variant Trx1P, as the two-proline variant Trx2P(P76P68) already folds seven times faster than Trx1P. trans-P34 also accelerates trans-to-cis isomerization of P76, albeit to a smaller extent. Overall, the results demonstrate that trans prolines can significantly modulate the kinetics of rate-limiting trans-to-cis proline isomerization in protein folding. Finally, we discuss possible mechanisms of acceleration and the potential significance of a protein-internal folding acceleration mechanism for Trx in a living cell.

A structural, DFT and experimental investigation of the ring stability and ring-opening polymerization behaviour of cyclic thionylphosphazenes in the presence of Lewis acid catalysts

A series of cyclic thionylphosphazenes were prepared and density functional theory (DFT) calculations initiated to gain insight into their susceptibility to ambient ring-opening polymerization with Lewis acid catalysts (GaCl3, AlCl3). DFT analyses determined that PBE1PBE-GD3BJ provided the optimal calculated structures for 1, 5, 5’ and 8. The gauge-independent atomic orbital (GIAO) method (M05-2X-GD3//PBE1PBE-GD3BJ) provided a good approximation for the 31P NMR resonances. Energy calculations indicate that thionylphosphazene phosphorus substitution promotes heterolytic cleavage of the thionyl S–Cl bond, as does adduct formation with GaCl3 or AlCl3, suggesting that 4 has potential for GaCl3-catalyzed ROP reactions at ambient temperatures. The generation of thionylphosphazene cation from 1 with catalytic quantities of Lewis acids (10:1 GaCl3, AlCl3) initiates the ambient temperature ROP to poly(thionylphosphazene) (2) in a minimum amount of solvent. Polymerization/depolymerization studies of 1 and 2 in solution was found to be fully reversible in the presence of GaCl3.

Simultaneous determination of multiple coupling networks by high-resolution 2D J-edited NMR spectroscopy

J coupling constitutes an important NMR parameter for molecular-level composition analysis and conformation elucidation. Dozens of J-based approaches have been exploited for J coupling measurement and coupling network determination, however, they are generally imposed to insufficient spectral resolution to resolve crowded NMR resonances and low measurement efficiency that a single experiment records one J coupling network. Herein, we propose a general NMR method to collect high-resolution 2D J-edited NMR spectra, which are characterized with advantages of pure absorptive lineshapes, decoupled chemical shift dimension, as well as eliminated axial peaks, thus facilitating J coupling partner assignments and J coupling constant measurements. More meaningfully, this protocol allows simultaneous determination of multiple coupling networks for highly efficient multiplet analyses via addressing multiple protons within one single experiment. Additionally, another variant is proposed for high-resolution applications under adverse magnetic field conditions. Therefore, this study provides a useful NMR protocol for configurational and structural studies with extensive applications in chemistry, biology, and material science.

Observability of Paramagnetic NMR Signals at over 10 000 ppm Chemical Shifts

AbstractWe report an experimental observation of 31P NMR resonances shifted by over 10 000 ppm (meaning percent range, and a new record for solutions), and similar 1H chemical shifts, in an intermediate‐spin square planar ferrous complex [tBu(PNP)Fe‐H], where PNP is a carbazole‐based pincer ligand. Using a combination of electronic structure theory, nuclear magnetic resonance, magnetometry, and terahertz electron paramagnetic resonance, the influence of magnetic anisotropy and zero‐field splitting on the paramagnetic shift and relaxation enhancement is investigated. Detailed spin dynamics simulations indicate that, even with relatively slow electron spin relaxation (T1 ≈10−11 s), it remains possible to observe NMR signals of directly metal‐bonded atoms because pronounced rhombicity in the electron zero‐field splitting reduces nuclear paramagnetic relaxation enhancement.

Observability of Paramagnetic NMR Signals at over 10 000 ppm Chemical Shifts.

We report an experimental observation of 31P NMR resonances shifted by over 10 000 ppm (meaning percent range, and a new record for solutions), and similar 1H chemical shifts, in an intermediate‐spin square planar ferrous complex [ tBu(PNP)Fe‐H], where PNP is a carbazole‐based pincer ligand. Using a combination of electronic structure theory, nuclear magnetic resonance, magnetometry, and terahertz electron paramagnetic resonance, the influence of magnetic anisotropy and zero‐field splitting on the paramagnetic shift and relaxation enhancement is investigated. Detailed spin dynamics simulations indicate that, even with relatively slow electron spin relaxation (T 1 ≈10−11 s), it remains possible to observe NMR signals of directly metal‐bonded atoms because pronounced rhombicity in the electron zero‐field splitting reduces nuclear paramagnetic relaxation enhancement.

Asporychalasin, a bioactive cytochalasan with an unprecedented 6/6/11 skeleton from the Red Sea sediment Aspergillus oryzae

The cytochalasan asporychalasin (1) was obtained from the marine fungus Aspergillus oryzae, isolated from the Red Sea sediments collected off Jeddah, Saudi Arabia. The chemical structure of 1 was elucidated by extensive spectroscopic analysis and quantum-mechanical calculations of 13C NMR resonances and ECD to possess an unprecedented 6/6/11-fused tricyclic skeleton, including an isoquinolindione ring in place of the typical isoindolone. Asporychalasin exhibited moderate antiproliferative activity against three human cancer cell lines, lung carcinoma (A549), liver carcinoma (HepG2), and breast carcinoma (MCF7), and no toxicity on zebrafish embryos.

What Is Being Measured with P-Bearing NMR Probe Molecules Adsorbed on Zeolites?

Elucidating the nature, strength, and siting of acid sites in zeolites is fundamental to fathom their reactivity and catalytic behavior. Despite decades of research, this endeavor remains a major challenge. Trimethylphosphine oxide (TMPO) has been proposed as a reliable probe molecule to study the acid properties of solid acid catalysts, allowing the identification of distinct Brønsted and Lewis acid sites and the assessment of Brønsted acid strengths. Recently, doubts have been raised regarding the assignment of the 31P NMR resonances of TMPO-loaded zeolites. Here, it is shown that a judicious control of TMPO loading combined with two-dimensional 1H-31P HETCOR solid-state NMR, DFT, and ab initio molecular dynamics (AIMD)-based computational modeling provides an unprecedented atomistic description of the host-guest and guest-guest interactions of TMPO molecules confined within HZSM-5 molecular-sized voids. 31P NMR resonances usually assigned to TMPO molecules interacting with Brønsted sites of different acid strength arise instead from both changes in the probe molecule confinement effects at ZSM-5 channel system and the formation of protonated TMPO dimers. Moreover, DFT/AIMD shows that the 1H and 31P NMR chemical shifts strongly depend on the siting of the framework aluminum atoms. This work overhauls the current interpretation of NMR spectra, raising important concerns about the widely accepted use of probe molecules for studying acid sites in zeolites.

Phomaligols F–I, polyoxygenated cyclohexenone derivatives from marine-derived fungus Aspergillus flavus BB1

By tracing the 13C NMR resonances for carbonyls and enols, four new oxidized phomaligol derivatives, phomaligols F–I (1–4), along with seven known compounds (5–11) were isolated from the culture of the fungus Aspergillus flavus BB1 isolated from the marine shellfish Meretrix meretrix collected on Hailing Island, Yangjiang, China. The chemical structures and the absolute configurations of the new compounds were elucidated by MS, NMR, ECD, optical rotation, and 13C NMR calculations. Compounds 1 and 2 represent the first examples of phomaligol derivatives that contain an unusual bicyclic skeleton. All isolated compounds were tested for their cytotoxic activity. Among them, sporogen-AO 1 (8) showed potent inhibitory activity against the cancer cell lines A549, H1299, SK-BR-3, and HCT116 with IC50 values of 0.13, 0.78, 1.19, and 1.32 μM, respectively. Phomaligol G (2) displayed cytotoxic activity against the A549 and H1299 cell lines with IC50 values of 46.86 and 51.87 μM respectively. Additionally, phomaligol H (3) demonstrated cytotoxic activity against the A549 cell line with an IC50 value of 65.53 μM. Mechanistic studies of compound 8 showed that it induced apoptosis of HCT116 cells in a dose-dependent manner.

NMR resonance assignments of human Atg3 in aqueous solution and bicelles.

Human Atg3 (hAtg3) is an E2-like enzyme that catalyzes the conjugation of LC3 family proteins to phosphatidylethanolamine (PE) lipids in the autophagosomal membrane during autophagy. The reaction product, LC3-PE, acts as a marker for autophagic cargo and is required for the effective construction of functional autophagosomes. However, the structural and molecular basis of this conjugation reaction remains elusive, at least in part, because of the absence of lipid bilayers in structural studies conducted to date. Here, we report a sequential resonance assignment for an hAtg3 construct both in aqueous solution and in bicelles. hAtg3 has 314 residues, and our construct lacks the unstructured region from residues 90 to 190. Our results demonstrate a structural rearrangement of hAtg3 N-terminus when it interacts with membranes.

Multiplet analysis by strong-coupling-artifact-suppression 2D J-resolved NMR spectroscopy.

Benefitting from the capability of recording scalar (J) couplings and bonding information, 2D J-resolved NMR spectroscopy constitutes an important tool for molecular structure analysis and mixture component identification. Unfortunately, conventional 2D J-resolved experiments generally encounter challenges of insufficient spectral resolution and strong coupling artifacts. In this study, a general NMR approach is exploited to record absorption-mode artifact-free 2D J-resolved spectra. This proposal adopts the advanced triple-spin-echo pure shift yielded by chirp excitation element to eliminate J coupling splittings and preserve chemical shifts along the F2 dimension, and it additionally utilizes the echo-train J acquisition to reveal the multiplet structure along the F1 dimension in accelerated experimental acquisition. Thus, it permits one to extract multiplet structure information from crowded spectral regions in one-shot experiments, with considerable resolution advantage resulting from completely decoupling F2 dimension and absorption-mode presentation, thus facilitating analysis on complex samples. More importantly, this method grants the superior performance on suppressing strong coupling artifacts, which have been affirmed by experiments on a series of chemical samples. As a consequence, this proposed method serves as a useful tool for J coupling measurements and multiplet structure analyses on complex samples that contain crowded NMR resonances and strong coupling spin systems, and it may exhibit broad application potentials in fields of physics, chemistry, and medical science, among others.

Sydnone Methides-A Forgotten Class of Mesoionic Compounds for the Generation of Anionic N-Heterocyclic Carbenes.

Sydnone methides are described from which only one single example has been mentioned in the literature so far. Their deprotonation gave anions which can be formulated as π‐electron rich anionic N‐heterocyclic carbenes. Sulfur and selenium adducts were stabilized as their methyl ethers, and mercury, gold as well as rhodium complexes of the sydnone methide carbenes were prepared. Sydnone methide anions also undergo C−C coupling reactions with 1‐fluoro‐4‐iodobenzene under Pd(PPh3)4 and CuBr catalysis. 77Se NMR resonance frequencies and 1 J C4‐Se as well as 1 J C4‐H coupling constants have been determined to gain knowledge about the electronic properties of the anionic N‐heterocyclic carbenes. The carbene carbon atom of the sydnone methide anion 3 j resonates at δ=155.2 ppm in 13C NMR spectroscopy at −40 °C which is extremely shifted upfield in comparison to classical N‐heterocyclic carbenes.

1H, 13C, 15N backbone and side-chain chemical shift assignments of the polyketide cyclase from Mycobacterium tuberculosis.

Polyketide cyclase from Mycobacterium tuberculosis (MtPC) is related to the formation of sterol derivatives, which may play a role in immune escape in the initial stage of macrophage infection by Mycobacterium tuberculosis. However, the structure and specific functions of MtPC are still unknown. Here we report the backbone and side-chain NMR resonance assignments for the MtPC. Most resonances were assigned and the secondary structure was predicted according to the assigned backbone resonances by TALOS-N and PECAN. These NMR assignments represent a first step towards researching the structure and function of MtPC.