NMR Crystallography Research Articles

Exploring Charge Redistribution at the Cu/Co6Se8 Interface.

This study investigates the electronic interactions and charge redistribution at the dopant-support interface using a Cu/Co6Se8 cluster construct. Specifically, the redox cluster series [Cu3Co6Se8L6]n ([1-Cu3]n; n = 0, -1, -2, -3; L = Ph2PNTol-, Ph = phenyl, Tol = p-tolyl) spanning four distinct oxidation states is synthesized and characterized using a multitude of techniques, including multinuclear NMR, UV-vis, XANES, and X-ray crystallography. Structural investigations indicate that the clusters are isostructural and chiral, adopting a pseudo-D3 symmetry. Paramagnetic 31P NMR spectroscopy and solution-phase magnetic measurements together with DFT calculations are employed to interrogate the electronic structure and spin-state changes across the [1-Cu3]3- to 1-Cu3 redox series, revealing that the copper edge sites retain a +1 oxidation state while the Co/Se core becomes increasingly oxidized, yielding a highly zwitterionic cluster.

Diastereomeric pure pyrazolyl-indolyl dihydrofurans: Unveiling isomeric selectivity in antibacterial action via in vitro and in silico insights

Developing pure diastereoisomeric molecular hybrids for the selective inhibition of bacterial growth opened new avenues for combating the ever-increasing microbial resistance. Considering this, a series of diastereoisomeric pure pyrazolyl-dihydrofurans (7a-7y) were synthesized and characterized using NMR, LCMS, and X-ray crystallography. DFT based method was used to explore the configurational stability of cis over trans isomeric form. Considering 7a and 8a as representative isomeric forms with same structural framework, the difference in their bio-efficacy against bacterial and fungal strains was assessed using serial dilution method. The relatively high inhibition of bacterial growth by the cis isomeric form (7a) (MIC = 1.562 µg/mL), amoxicillin (MIC = 3.125 µg/mL) inspired us to broaden the substrate scope for synthesizing a series of pure diastereoisomeric cis forms as selective anti-bacterial agents. However, both the isomers displayed antifungal activity less than the standard drug (Fluconazole) employed in the study. All the reactions proceeded smoothly and yielded a diverse array of dihydrofuran derivatives. The developed synthetics were found to be non-cytotoxic against mouse fibroblast cells and didn’t affect the seed germination of Brassica nigra seeds when treated at a concentration of 1 mg/mL. The experimentally determined in vitro results were further validated using in silico molecular docking and dynamics studies.

Sucurchalasins A and B, Sulfur-Containing Heterodimers of a Cytochalasan and a Macrolide from the Endophytic Fungus Aspergillus spelaeus GDGJ-286.

Two sulfur-containing heterodimers of a cytochalasan and a macrolide, sucurchalasins A and B (1 and 2), and four known cytochalasan monomers (3-6), as well as four known macrolide derivatives (7-10), were obtained from the endophytic fungus Aspergillus spelaeus GDGJ-286. Sucurchalasins A and B (1 and 2) are the first cytochalasan heterodimers formed via a thioether bridge between cytochalasan and curvularin macrolide units. Their structures were elucidated by detailed analysis of NMR, LC-MS/MS, and X-ray crystallography. In bioassays, 1 and 2 exhibited cytotoxic effects on A2780 cells, with IC50 values of 3.9 and 8.3 μM, respectively. They also showed antibacterial activities against E. faecalis and B. subtilis with MIC values of 3.1 and 6.3 μg/mL, respectively.

Naked eye Fe(III) recognition and anticancer efficacy evaluation via diazenyl-propargyl appended imine functionalized moiety

The study delves into the synthesis of diazenyl-propargyl appended imine functionalized moiety (4) emphasizing its structural dynamic, Fe(III) sensitivity, and anticancer potential. The synthesized compound was characterized via NMR (1H,13C), TGA, mass spectrometry, and single-crystal X-ray crystallography. The color transition of the compound from yellow to red demonstrates naked-eye sensing for Fe (III), validated by UV–visible spectroscopy. The limit of detection (LOD) and Association Constant (Ka) were calculated from the linear calibration curve and the B–H plot come out to be 28.71 nM and 2.17 × 105 M−1, respectively. As per Job’s plot Fe(III) binds to probe (4) in 1:1 stoichiometry. The interaction of probe (4) with Fe(III) has been examined through VSM (vibrating spectrum magnetism) study, FT-IR, 1H NMR and mass spectrometry. The pharmacokinetic properties of the synthesized compound were assessed, emphasizing absorption, distribution, metabolism, excretion and toxicity. The cytotoxicity assay using SAF-1 cell line indicated that the compound is nontoxic. Also compound (4) showed positive response on cervical cancer cells line and this anti-cancer potential has been further explored through molecular docking analysis.

Unusual norcucurbitacin glycosides from the roots of Siraitia grosvenorii

Siraitia grosvenorii Swingle is one of the first approved medicine food homology species in China, and it has been used as a natural sweetener in the food industry and as a traditional medicine to relieve cough and reduce phlegm. However, many S. grosvenorii roots are discarded yearly, which results in a great waste of resources. Twelve undescribed norcucurbitacin-type triterpenoid glycosides, siraitiaosides A-L (1–12), and six known analogs (13–18) were isolated from the roots of S. grosvenorii. The structures of isolated norcucurbitacin glycosides were elucidated by comprehensive data analyses, including HRESIMS, UV, IR, NMR, ECD calculations, and X-ray crystallography analysis. Siraitiaosides A-E (1–5) featured an unusual 19,29-norcucurbitacin framework while siraitiaosides F-L (6–12) featured a rare 29-norcucurbitacin framework. Notably, compound 4 displayed moderate anti-acetylcholinesterase (AChE) activity with an IC50 of 21.0 μM, meanwhile, compounds 16 and 18 exhibited pronounced cytotoxic activities against MCF-7, CNE-1, and HeLa cancer cell lines with IC50 values of 2.1–15.2 μM. In silico studies showed that compound 4 bound closely to AChE with a binding energy of −5.04 kcal/mol, and compound 18 could tightly bind to PI3K, AKT1, ERK2, and MMP9 proteins that related to autophagy, apoptosis, migration/invasion, and growth/proliferation. In summary, the roots of Siraitia grosvenorii have potential medicinal values due to the multiple bioactive components.

Unraveling biological disparities in configurational isomers of pyrazolyl-dihydrofurans using in vitro, DFT and in silico approach

The biological disparities in the high activity of one isomeric form over another have attracted significant interest from medicinal chemists and opened new avenues for synthesizing pure diastereoisomeric drugs.A series of diastereoisomeric pure pyrazolyl-dihydrofurans (6a-6ae) were synthesized in good to excellent yields, and their structures were determined using NMR, LCMS and X-ray crystallography. The difference in the stability of cis and trans isomers has been established using DFT-based studies. Using the serial dilution method, the developed synthetics were evaluated for their bio-efficacy against bacterial and fungal strains. The cytotoxicity was evaluated against mouse fibroblast cells as well as using the seed germination method.All the reactions proceeded smoothly and resulted into cis as the significant isomer; the stability over trans isomer has been established using DFT-based computational studies. Considering 6a and 7a as prototype, the difference in their biological response has been evaluated through in vitro anti-microbial assay. A significant difference in the biological activity has been observed, as the cis isomer (6a) has been found to be more potent over its respective trans isomer (7a) in bacterial assay. As far as the fungal response is concerned, no difference in their biological activity has been observed. The investigated compounds are non-cytotoxic against mouse fibroblast cells and Brassica nigra seeds. The experimentally determined in vitro results have been established using in silico studies.The cis isomer (6a) with an MIC of 3.25 µg/mL has been found to be more potent than the respective trans (7a) form (MIC = 6.25–12.5 µg/mL) when evaluated against different gram positive and negative strains utilized in the present study. However, no disparity in their biological response has been observed in fungal studies.

Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination

Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.

Mono- and Bis-Phosphine Promoted Incorporation of Boron, Nitrogen, and Phosphorus into Heterocycles via Staudinger Reactions of Borafluorene Azides.

We report the synthesis and characterization of a series of BNP-incorporated borafluorenate heterocycles formed via thermolysis reactions of pyridylphosphine and bis(phosphine)-coordinated borafluorene azides. The use of diphenyl-2-pyridylphosphine (PyPh2P), trans-1,2-bis(diphenylphosphino)ethylene (Ph2P(H)C═C(H)PPh2), and bis(diphenylphosphino)methane (Ph2PC(H2)PPh2) as stabilizing ligands resulted in Staudinger reactions to form complex heterocycles with four- (BN2P, BNPC, P2N2) and five-membered (BNP2C and BN2PC) rings, which were successfully isolated and fully characterized by multinuclear NMR and X-ray crystallography. However, when bis(diphenylphosphino)benzene (Ph2P-Ph-PPh2) was used as the ligand in a reaction with 9-bromo-9-borafluorene (BF-Br), due to the close proximity of the donor P atoms, the diphosphine-stabilized borafluoronium ion with an unusual borafluorene dibromide anion was formed. Reaction of the borafluoronium ion with trimethylsilyl azide left the cation intact, and the dibromide anion was substituted by a diazide. Density functional theory calculations were used to provide mechanistic insight into the formation of these new boracyclic compounds. This work highlights a new method in which donor phosphine ligands may be used to promote dimerization, cyclization, and ring contraction reactions to produce boracycles via Staudinger reactions.

Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins.

Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.

Competing electrophilic substitution and oxidative polymerization of arylamines with selenium dioxide.

This article describes the detailed analysis of the reaction between arylamines, such as aniline, o-anisidine, and methyl anthranilate, with selenium dioxide in acetonitrile. A systematic analysis of the reaction products with the help of 77Se NMR and single-crystal X-ray crystallography revealed that the reaction progress follows three major reaction pathways, electrophilic selenation, oxidative polymerization, and solvent oxidation. For aniline and o-anisidine, predominant oxidative polymerization occurred, leading to the formation of the respective polyaniline polymers as major products. For methyl anthranilate, the oxidative polymerization was suppressed due to the delocalization of amine lone pair electrons over the adjacent carboxylate function, which prompted the selenation pathway, leading to the formation of two of the isomeric diorganyl selenides of methyl anthranilate. The diaryl selenides were structurally characterized using single-crystal X-ray diffraction. Density functional theory calculations suggest that the highest occupied molecular orbital of methyl anthranilate was deeply buried, which suppressed the oxidative polymerization pathway. Due to solvent oxidation, oxamide formation was also noticed to a considerable extent. This study provides that utmost care must be exercised while using SeO2 as an electrophile source in aromatic electrophilic substitution reactions.

11-Hydroxy-7-Methoxy-2,8-Dimethyltetracene-5,12-Dione

Microorganisms are a valuable source of pharmaceutically active chemicals, serving as scaffolds for synthesis as well as lead structures. Investigating novel biomes frequently yields intriguing chemistry; the Atacama Desert in Chile is one such example. This study reports the isolation of a new reduced anthracycline-related compound from the Atacama Desert-derived bacterium Saccharothrix S26. Structural characterisation was achieved by one-dimensional and two-dimensional NMR, HR-LCMS, and X-ray crystallography. The compound was tested against the ESKAPE pathogens, bovine mastitis-related pathogens, and the fungal strain Cryptococcus neoformans, but no antimicrobial activity was observed.

High-Resolution 17O Solid-State NMR as a Unique Probe for Investigating Oxalate Binding Modes in Materials: The Case Study of Calcium Oxalate Biominerals.

Oxalate ligands are found in many classes of materials, including energy storage materials and biominerals. Determining their local environments at the atomic scale is thus paramount to establishing the structure and properties of numerous phases. Here, we show that high-resolution 17O solid-state NMR is a valuable asset for investigating the structure of crystalline oxalate systems. First, an efficient 17O-enrichment procedure of oxalate ligands is demonstrated using mechanochemistry. Then, 17O-enriched oxalates were used for the synthesis of the biologically relevant calcium oxalate monohydrate (COM) phase, enabling the analysis of its structure and heat-induced phase transitions by high-resolution 17O NMR. Studies of the low-temperature COM form (LT-COM), using magnetic fields from 9.4 to 35.2 T, as well as 13C-17O MQ/D-RINEPT and 17O{1H} MQ/REDOR experiments, enabled the 8 inequivalent oxygen sites of the oxalates to be resolved, and tentatively assigned. The structural changes upon heat treatment of COM were also followed by high-resolution 17O NMR, providing new insight into the structures of the high-temperature form (HT-COM) and anhydrous calcium oxalate α-phase (α-COA), including the presence of structural disorder in the latter case. Overall, this work highlights the ease associated with 17O-enrichment of oxalate oxygens, and how it enables high-resolution solid-state NMR, for "NMR crystallography" investigations.

5,6-Diphenyl-1,3,4,7-tetra-p-tolyl-1,3,3a,7a-tetrahydropentaleno[1,2-c]furan

The reaction of (Z)-5-phenyl-1,3-di-p-tolylpent-2-en-4-yn-1-ol (1) with trimethylsilyl chloride in dichloromethane at ambient temperature gave a dimeric ether compound 2 in 30% yield. Subsequently, heating 2 in toluene under refluxing temperature rendered the title compound quantitatively. The structure of this tricyclic-fused compound was characterized using NMR, mass spectroscopy, and X-ray crystallography. This unique linear tricyclic fused furan framework is reported for the first time.

Daphmacrimines A−K, Daphniphyllum alkaloids from Daphniphyllum macropodum Miq

Daphmacrimines A–K (1–11) were isolated from the leaves and stems of Daphniphyllum macropodum Miq. Their structures and stereochemistries were determined by extensive techniques, including HRESIMS, NMR, ECD, IR, and single-crystal X-ray crystallography. Daphmacrimines A–D (1–4) are unprecedented Daphniphyllum alkaloids with a 2-oxazolidinone ring. Daphmacrimine I (9) contains a nitrile group, which is relatively rare in naturally occurring alkaloids. The abilities of daphmacrimines A–D and daphmacrimines G–K to enhance lysosomal biogenesis were evaluated through LysoTracker Red staining. Daphmacrimine K (11) can induce lysosomal biogenesis and promote autophagic flux.

Unveiling the antimicrobial potency and binding interaction between sulfonamide substituted Schiff’s bases and BSA protein: An integrated experimental and theoretical approach

Sulfonamide derived Schiff’s bases encompass significant properties such as antifungal, anti-inflammatory, anticancer, antibacterial, antiproliferative, and antioxidant and hold a central position in therapeutics and diagnostics. Hence, it is essential to comprehend their interconnection with carrier proteins such as Bovine serum albumin (BSA). Herein, two different sulfonamide derived Schiff’s base derivatives,N'-(2,5-Dimethoxybenzylidene)-4-methylbenzenesulfonohydrazide SB-1 and N'-(3-Bromo-4-methoxybenzylidene)-4-methylbenzenesulfonohydrazide SB-2 were synthesized by reacting respectivealdehydes with p-toluenesulfonyl hydrazide as the amine counterpart in absolute ethanol and structurally characterized by FT-IR,1H and13C NMR, elemental analyses, thermogravimetric analysis (TGA), mass spectrometry and single-crystal X-ray crystallography. The binding interactions between BSA andSB-1 and SB-2were made by employing UV–vis. absorption and fluorescence spectroscopy. Information about the binding constant was obtained from the absorbance enhancement and fluorescence quenching of BSA in the presence ofSB-1 and SB-2respectively. However, the binding efficiency ofSB-1was found to be superior to that of BSA in comparison toSB-2. The antibacterial potential ofSB-1 and SB-2 wastested on E. coliandS. aureus using thewell diffusion method.In silicoADME properties forSB-1 and SB-2were checked to assess their stability. The binding mechanisms to the specific enzymes associated with the BSA interaction and the antibacterial capabilities of theSB-1 and SB-2were further supported by molecular docking calculations. The detailed studies provide comprehensive data to support the utility of prepared Schiff’s bases as potential biomarkers in therapeutics.

1-(2,4-Dinitrophenyl)-2-((Z)-2-((E)-4-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-ylidene)hydrazine

The reaction of (E)-2-(4-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-one and (2,4-dinitrophenyl)hydrazine in boiling ethanol containing hydrochloric acid (0.2 mL; 37%) for 1.5 h gave 1-(2,4-dinitrophenyl)-2-(2-(4-fluorobenzylidene)-3,4-dihydronaphthalen-1(2H)-ylidene)hydrazine in a 90% yield. Various spectral analyses, including NMR, and X-ray crystallography established the structure of the newly synthesized hydrazone.

Carbon-Sulfur Bond Cleavage in Methanesulfonate on Diorganotin Quinaldate Platform - Synthesis and Characterization of [(n-Bu2SnL)2SO4

The synthesis of mixed ligand di-n-butyltin complexes, [(n-Bu2SnL1-3)2SO4], 2-4 (HL1-3=2-quinoline/ 1-isoquinoline/ 4-methoxy-2-quinoline carboxylic acid) has been realized by reacting n-Bu2Sn(OMe)OSO2Me, 1 a with the corresponding quinaldic acid under solvothermal conditions. The observed transformation of methane sulfonate to sulfate anion represents a rare example of C-S bond cleavage on the organotin scaffolds, n-Bu2Sn(L1-3)OSO2Me, which have been identified as en route intermediates by NMR and X-ray crystallography. Analogous reaction when extended with Me2Sn(OMe)OSO2Me, 1 b and HL2 yields [(Me2Sn)2(L2)3(OSO2Me)], 5 as partially disproportionated product of Me2Sn(L2)OSO2Me. The solid-state structures of 2-5 reveal variable modes of coordination of the ligands to afford molecular and polymeric motifs.

Asymmetric synthesis, characterization of chiral trans and cis-3-chloro/oxo/thio-4-styryl-β-lactams using (R)-(+)-1-phenylethylamine and their efficient column chromatographic separation

Diverse chiral trans and cis-3-chloro/oxo/thio-4-styryl-β-lactams were efficiently synthesized using chiral 3′-phenylallylidene-[(R)-1′-phenylethyl] amine and substituted ethanoic acids. Moore ketenes derived from chloro/phenythio/benzylthio ethanoic acids (Cl/PhS/BzS) affords both chiral trans- and cis β-lactams, with a preference for trans-stereochemistry. However, Bose-Evans ketenes obtained from 2-methoxy/phenoxyethanoic acids (MeO/PhO), led to the exclusive formation of cis-diastereomers only. Further, individual diastereomers of trans- and cis-β-lactams were separated via efficient column chromatography. The relative cis and trans configuration of the C-3 and C-4 protons in chiral β-lactams was established using coupling constant value ranging from J = 1.4 to 2.1 Hz (in case of trans) and J = 4.3 to 5.2 Hz (in case of cis) respectively. Structural confirmation of β-lactams was done using FT-IR, NMR (1H,13C,1H-1H COSY and 1H-13C HSQC), elemental analysis, ESI-MS and X-ray crystallography.

2,3,5,6-Tetrafluoro-[N-(3-aminopropyl)-ε-caprolactam]-4-pyridine

The title compound was synthesized at a near-quantitative yield using the nucleophilic aromatic substitution of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) with perfluoropyridine (PFP). The purity and structure were determined by NMR (1H, 13C, 19F), GC-EIMS, and single-crystal X-ray crystallography.

NMR crystallography of amino acids

The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.