Power of isotopic fine structure for unambiguous determination of metabolite elemental compositions: In silico evaluation and metabolomic application

In mass spectrometry (MS)-based metabolomics studies, reference-free identification of metabolites is still a challenging issue. Previously, we demonstrated that the elemental composition (EC) of metabolites could be unambiguously determined using isotopic fine structure, observed by ultrahigh resolution MS, which provided the relative isotopic abundance (RIA) of ¹³C, ¹⁵N, ¹⁸O, and ³⁴S. Herein, we evaluated the efficacy of the RIA for determining ECs based on the MS peaks of 20,258 known metabolites. The metabolites were simulated with a ≤25% error in the isotopic peak area to investigate how the error size effect affected the rate of unambiguous determination of the ECs. The simulation indicated that, in combination with reported constraint rules, the RIA led to unambiguous determination of the ECs for more than 90% of the tested metabolites. It was noteworthy that, in positive ion mode, the process could distinguish alkali metal-adduct ions ([M + Na]⁺ and [M + K]⁺). However, a significant degradation of the EC determination performance was observed when the method was applied to real metabolomic data (mouse liver extracts analyzed by infusion ESI), because of the influence of noise and bias on the RIA. To achieve ideal performance, as indicated in the simulation, we developed an additional method to compensate for bias on the measured ion intensities. The method improved the performance of the calculation, permitting determination of ECs for 72% of the observed peaks. The proposed method is considered a useful starting point for high-throughput identification of metabolites in metabolomic research.     

Control of Axial Chirality by Planar Chirality Based on Optically Active [2.2]Paracyclophane

Optically active X-shaped molecules based on the planar chiral [2.2]paracyclophane building block were prepared, in which di(methoxy)terphenyl units were stacked on the central benzene rings. At 25 °C, anisolyl rings freely rotate in solution, while in the crystal form, they are fixed by intramolecular CH–π interactions, thereby leading to the expression of the axial chirality, i.e., propeller chirality was exhibited by the planar chiral [2.2]paracyclophane moiety. The X-shaped molecule exhibited good circularly polarized luminescence (CPL) profiles with moderate Φ_PL and a large g_lum value in the order of 10⁻³ at 25 °C, in solution. In contrast, at −120 °C, dual CPL emission with opposite signs was observed. According to the theoretical studies, the rotary motion of the anisolyl units is suppressed in the excited states, and so emission from two isomers could be observed. These results demonstrate that the axial chirality was controlled by the planar chirality, leading ultimately to propeller chirality.     

Absolute configuration of pterocidin,a potent inhibitor of tumor cell invasion from a marine-derived Streptomyces

During the course of screening natural products for the inhibitors of tumor cell invasion, pterocidin, a linear polyketide with a δ-lactone terminus, was rediscovered from a Streptomyces strain of a marine sediment-origin. A series of J-based configuration analyses and NOESY analysis, coupled with chemical derivatization and chiral anisotropy analysis, established the absolute stereochemistry of five asymmetric centers in this compound.     

Encapsulation and Enhanced Luminescence Properties of IrIII Complexes within a Hexameric Self‐Assembled Capsule

Encapsulation and luminescence studies of [Ir(ppy)₂(bpy)]Cl (ppy=2‐phenylpyridinate, bpy=2,2′‐bipyridine) within a hexameric resorcinarene capsule are reported. One Ir^III complex cation was encapsulated within the capsule, as demonstrated by NMR and dynamic light scattering (DLS) studies. The emission color of the Ir^III complex was drastically changed from orange to yellow by encapsulation, in contrast with the lack of significant changes in the absorption spectrum. The hexameric capsule effectively hampers the non‐radiative pathway to increase both the luminescence quantum yield and the exited state lifetime. The luminescent properties of the encapsulated Ir^III complex depend on the ratio of Ir^III complex to the resorcinarene monomer as well as the concentration of resorcinarene monomer owing to the reversible process of self‐assembly of the hexameric capsule. Quenching experiments revealed that the Ir^III complex in the capsule was effectively separated from quenchers.     

Thermal and optical properties of highly fluorinated copolymers of methacrylates

Copolymers of pentafluorophenylhexafluoroisopropyl methacrylate (FPPMA) with trifluoroethyl methacrylate (TFEMA) were prepared in THF solution and in bulk using azobisisobutyronitrile as a free radical initiator. The monomer reactivity ratios of TFEMA (M₁) and FPPMA (M₂) were calculated as r₁ = 0.55 and r₂ = 0.07. The refractive indices of poly(TFEMA) and poly(FPPMA) are very similar as 1.435 and 1.430, respectively, at 532 nm, and the copolymer films were transparent. The glass transition temperatures (T_g) of the copolymers were in the range of 80–90°C and showed a negative deviation from the Gordon–Taylor equation. The thermal decomposition temperature (T_d) was increased with the content of FPPMA in copolymers. Low water absorption for 1:1 FPPMA/TFEMA copolymer was detected. Copolymers of FPPMA with hexafluoroisopropyl methacrylate (HFPMA) were also prepared. The monomer reactivity ratios of HFPMA (M₁) and FPPMA (M₂) were calculated as r₁ = 0.43 and r₂ = 0.10. The T_gs of the copolymers were in the range of 88–95°C and showed also a negative deviation from the Gordon–Taylor equation. T_g and T_d of the copolymers were increased with the content of FPPMA. The refractive index of poly(HFPMA) (1.384 at 532 nm) is much lower than that of FPPMA homopolymer, but copolymer films obtained were clear and transparent. Copyright © 2013 John Wiley & Sons, Ltd.     

Quinone-recognition by Four-point Hydrogen Bonding in Porphyrin System Having Urea Moiety

5,15- cis -bis(Ureidophenyl)porphyrins have significant recognizing ability for p -benzoquinones through four-point hydrogen bonding. Although an unusual temperature-dependence of the complexation is observed with bis( N '-phenylureidophenyl) porphyrin, bis( N '-ethylureidophenyl)porphyrin shows a satisfactorily linear van't Hoff plot and recognizes an electron-rich p -benzoquinone such as tetramethyl- p -benzoquinone more effectively, which is ascribed to the large enthalpy change in the complex.     

Mannose‐Binding Geometry of Pradimicin A

Pradimicins (PRMs) and benanomicins are the only family of non‐peptidic natural products with lectin‐like properties, that is, they recognize D ‐mannopyranoside (Man) in the presence of Ca²⁺ ions. Coupled with their unique Man binding ability, they exhibit antifungal and anti‐HIV activities through binding to Man‐containing glycans of pathogens. Notwithstanding the great potential of PRMs as the lectin mimics and therapeutic leads, their molecular basis of Man recognition has yet to be established. Their aggregate‐forming propensity has impeded conventional interaction analysis in solution, and the analytical difficulty is exacerbated by the existence of two Man binding sites in PRMs. In this work, we investigated the geometry of the primary Man binding of PRM‐A, an original member of PRMs, by the recently developed analytical strategy using the solid aggregate composed of the 1:1 complex of PRM‐A and Man. Evaluation of intermolecular distances by solid‐state NMR spectroscopy revealed that the C2–C4 region of Man is in close contact with the primary binding site of PRM‐A, while the C1 and C6 positions of Man are relatively distant. The binding geometry was further validated by co‐precipitation experiments using deoxy‐Man derivatives, leading to the proposal that PRM‐A binds not only to terminal Man residues at the non‐reducing end of glycans, but also to internal 6‐substituted Man residues. The present study provides new insights into the molecular basis of Man recognition and glycan specificity of PRM‐A.