Related Isomers Research Articles

Tetragermacyclobutadiene: Energetically Disfavored with Respect to Its Structural Isomers

Germanium has been a central feature in the renaissance of main-group inorganic chemistry. Herein, we present the stationary-point geometries of tetragermacyclobutadiene and its related isomers on the singlet potential energy surface at the CCSD(T)/cc-pVTZ level of theory. Three of these 12 structures are reported for the first time and one of them is predicted to lie only 0.4 kcal mol(-1) above the previously reported global minimum. Focal-point analyses has provided electronic energies at the CCSD(T) level of theory, which are extrapolated to the complete basis-set limit and demonstrate the convergence behavior of the electronic energies with improving levels of theory and increasing basis-set size. The lowest-energy structure is the bicyclic structure, which lies 35 kcal mol(-1) below the "all-Ge" cyclobutadiene structure. The reaction energies for the association of known Ge hydrides (e.g., digermene) to form Ge4H4 indicate that Ge4H4 could be observed experimentally. We investigate the bonding patterns by examining the frontier molecular orbitals. Our results demonstrate that: 1) the cyclic isomers of (GeH)4 distort to maximize the mixing of the p orbitals that are involved in the π system of tetragermacyclobutadiene and 2) the lowest-energy isomers exhibit unusual bonding arrangements (e.g., bridging H bonds) that maximize the nonbonding electron density at the Ge centers.

Identification of isomeric disaccharides in mixture by the 1-phenyl-3-methyl-5-pyrazolone labeling technique in conjunction with electrospray ionization tandem mass spectrometry

1-Phenyl-3-methyl-5-pyrazolone (PMP) labeling technique has hitherto proved to be a convenient and sensitive method for separating and detecting oligosaccharides. However, the detailed fragmentation of the derivatives by tandem mass spectrometry has been reported limitedly and no characteristic fragment ions for isomers have been detected. In this study, eight disaccharide isomers were labeled with PMP and analyzed by positive ion electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn). In comparison with the native disaccharides, PMP labeled disaccharides gave rise to more fragment ions in the tandem mass spectra. The distinctive diagnostic fragment ions formed from cleavage of CC bonds have been detected in the fragmentation of PMP-labeled disaccharide linkage isomers, allowing unambiguous assignment of the position of the glycosidic linkages. This feature is particularly useful for the structural determination of unknown isomeric disaccharides mixed together. In addition, the anomeric configurations can also be easily assigned based on the relative abundance ratios of the selected ion pairs. To verify the feasibility of the method used in the analysis of natural product, water soluble Panax Ginseng extract has been further investigated to identify its unknown disaccharides. The results confirmed that the PMP labeling technique in conjunction with ESI-MSn could offer a powerful and convenient tool for differentiation of structurally closely related isomers, even the unknown mixtures of isomeric disaccharides with different linkage types.

Size Effects on Cation Heats of Formation. II. Methyl Substitutions in Oxygen Compounds

A relation between the heat of formation of molecular ions and cation size is used to study the effects of methyl substitution on a series of species containing oxygen. These include methanol, the hydroxymethyl radical, formaldehyde and related isomers, acetaldehyde and related isomers, ketene, formic acid, and acetic acid. This size-dependent relation is found to be valid in most cases, enabling a choice to be made among conflicting reported ion and neutral heat of formation values, but it holds much less well in methyl-substituted formaldehyde and its carbene isomers. The cations formed in methanol, hydroxymethyl, hydroxycarbene, and formic acid by methyl substitution at carbon sites were found to be more stable than those substituted at oxygen sites. Suggestions are made for investigating or reinvestigating the ionization energies and the heats of formation of several of the molecules studied in cases where multiple choices are available in the literature or where our analysis suggests that more reliable values are needed.

Application of Molecular Imprinted Polymer Solid Phase Extraction (MISPE) in the Extraction of Caffeine From Coffee

Caffeine is naturally found in plant products such as coffee beans, cocoa beans and tea leaves. In this study, caffeine molecular imprinted polymer (MIP) was synthesized by dissolving 1 mmol caffeine and 4 mmol monomer, methacrylic acid (MAA) and 1mmol ethylene glycol dimethacrylate (EDMA) as the crosslinker and benzoyl peroxide (BOP) as the initiator. MIP exhibits significantly high affinity and selectivity for the target analytes used as the template than for similar molecules, including closely related isomers. The efficiency of extraction using caffeine MIP as sorbents in solid phase extraction (SPE) was evaluated. Good recovery (91.6 %) and low percent RSD (0.9 %) was obtained using the spiked samples (10 µg/mL). The molecular imprinted polymer solid phase extraction (MISPE) technique was then applied in the extraction of caffeine from various coffee samples. Based on the excellent selectivity, MIP is a promising approach for the extraction of compounds from a complex matrix such as herbal extract.

Relative Stereochemical Determination and Synthesis of the C17–C25 δ-Lactone Fragment of Hemicalide

Hemicalide is a novel marine metabolite polyketide distinguished by a unique mechanism of action. Because of insufficient quantities of purified material, this natural product has evaded complete stereochemical assignments. Recently, we have determined the relative stereochemistry of the C8-C13 hexad by synthesizing the C1-C13 fragment. Presently, we report the assignment of the C17-C25 δ-lactone fragment. NMR analysis of authentic hemicalide along with a computational conformation study allowed us to reduce the number of putative relative isomers from 16 to 4. Concise syntheses of the four candidate diastereomers were achieved using a common strategy based on a Dias aldehyde allylation reaction, an intramolecular Horner-Wadsworth-Emmons olefination, and a dihydroxylation reaction. Finally, thorough NMR comparisons enabled us to deduce the relative stereochemistry of the C1-C17 fragment with high certainty.

The synthesis and characterisation of homo- and heterobimetallic 1,14,2,9- and 1,14,2,10-M2C2B1014-vertex metallacarboranes

A high-yielding synthesis of the 13-vertex cobaltacarborane 4-Cp-4,1,12-closo-CoC(2)B(10)H(12) is described and this compound used to prepare the known 14-vertex species 1,14-Cp(2)-1,14,2,10-closo-Co(2)C(2)B(10)H(12) (II) and 1-(p-cymene)-14-Cp-1,14,2,10-closo-RuCoC(2)B(10)H(12) (IV), the latter by a new route. The related species 1,14-Cp(2)-2,10-Me(2)-1,14,2,10-closo-Co(2)C(2)B(10)H(10) (1) and 1,14-(η-C(9)H(7))(2)-1,14,2,10-closo-Co(2)C(2)B(10)H(12) (2) are also reported. Polyhedral expansion of 4,1,8-CoC(2)B(10) compounds affords a different isomer of the 14-vertex bimetallacarboranes, 1,14,2,9-Co(2)C(2)B(10), and three examples, 1,14-Cp(2)-1,14,2,9-closo-Co(2)C(2)B(10)H(12) (3), 1,14-Cp(2)-2,9-Me(2)-1,14,2,9-closo-Co(2)C(2)B(10)H(10) (4) and 1,14-(η-C(9)H(7))(2)-1,14,2,9-closo-Co(2)C(2)B(10)H(12) (5), are prepared and characterised. Patterns in (11)B NMR chemical shifts and in <δ(11)B>, the weighted average (11)B chemical shift, within and between related isomers of the 14-vertex compounds II and 1-5 are discussed. Compounds II, IV, 2, 4 and 5 were studied crystallographically, with cage C atom positions in these and related bicapped hexagonal antiprismatic 1,14,2,x-M(2)C(2)B(10) species analysed by the Vertex-to-Centroid Distance method.

Biosynthesis, isolation, and NMR analysis of leukotriene A epoxides: substrate chirality as a determinant of the cis or trans epoxide configuration

Leukotriene (LT)A₄ and closely related allylic epoxides are pivotal intermediates in lipoxygenase (LOX) pathways to bioactive lipid mediators that include the leukotrienes, lipoxins, eoxins, resolvins, and protectins. Although the structure and stereochemistry of the 5-LOX product LTA₄ is established through comparison to synthetic standards, this is the exception, and none of these highly unstable epoxides has been analyzed in detail from enzymatic synthesis. Understanding of the mechanistic basis of the cis or trans epoxide configuration is also limited. To address these issues, we developed methods involving biphasic reaction conditions for the LOX-catalyzed synthesis of LTA epoxides in quantities sufficient for NMR analysis. As proof of concept, human 15-LOX-1 was shown to convert 15S-hydroperoxy-eicosatetraenoic acid (15S-HPETE) to the LTA analog 14S,15S-trans-epoxy-eicosa-5Z,8Z,10E,12E-tetraenoate, confirming the proposed structure of eoxin A₄. Using this methodology we then showed that recombinant Arabidopsis AtLOX1, an arachidonate 5-LOX, converts 5S-HPETE to the trans epoxide LTA₄ and converts 5R-HPETE to the cis epoxide 5-epi-LTA₄, establishing substrate chirality as a determinant of the cis or trans epoxide configuration. The results are reconciled with a mechanism based on a dual role of the LOX nonheme iron in LTA epoxide biosynthesis, providing a rational basis for understanding the stereochemistry of LTA epoxide intermediates in LOX-catalyzed transformations.

Distribution of long chain heterocyst glycolipids in cultures of the thermophilic cyanobacterium Mastigocladus laminosus and a hot spring microbial mat

The intact polar lipid (IPL) composition of a microbial mat growing in a sulfidic Icelandic hot spring at 55°C was investigated. The composition was dominated by the glycolipids monoglycosyldiacylglycerol (MGDG), diglycosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG) and the glycerophospholipid phosphatidylglycerol (PG). We also detected a series of heterocyst glycolipids (HGs) with an elongated aglycone moiety via comparison with those found in other microbial mats. Based on the mass spectra, we identified the components as 1-(O-hexose)-3,27,29-triacontanetriol (C30 HG triol) and 1-(O-hexose)-3,29,31-dotriacontanetriol (C32 HG triol). The principal mat builders were the thermophilic heterocystous cyanobacterium Mastigocladus laminosus (Stigonematales) and green nonsulfur-like bacteria (GNSLB) closely related to Chloroflexus aurantiacus. Since HGs are characteristic lipids for heterocystous cyanobacteria, M. laminosus is the likely source of the long chain HGs. IPL analysis of cultivated M. laminosus confirmed that this heterocystous cyanobacterium synthesized the C32 HG triol and a related isomer. Culture experiments at different growth temperatures showed no change in the overall HG composition but revealed that the relative proportion of the different C32 HG triol isomers varied, possibly as a physiological response to maintaining sub-μM O2 concentration within the heterocyst. Combined with previous studies, our results suggests that the C32 HG triol might be of chemotaxonomic value for identifying heterocystous cyanobacteria of the order Stigonematales in hot spring and other microbial mats.

Erratum: Relative Isomer Abundance of Fullerenes and Carbon Nanotubes Correlates with Kinetic Stability [Phys. Rev. Lett.107, 175506 (2011)

Erratum: Relative Isomer Abundance of Fullerenes and Carbon Nanotubes Correlates with Kinetic Stability [Phys. Rev. Lett.<b>107</b>, 175506 (2011)

Optimization of a Genetic Algorithm for the Functionalization of Fullerenes.

We present the optimization of a genetic algorithm (GA) that is designed to predict the most stable structural isomers of hydrogenated and hydroxylated fullerene cages. Density functional theory (DFT) and density functional tight binding (DFTB) methods are both employed to compute isomer energies. We show that DFTB and DFT levels of theory are in good agreement with each other and that therefore both sets of optimized GA parameters are very similar. As a prototypical fullerene cage, we consider the functionalization of the C20 species, since for this smallest possible fullerene cage it is possible to compute all possible isomer energies for evaluation of the GA performance. An energy decomposition analysis for both C20Hn and C20(OH)n systems reveals that, for only few functional groups, the relative stabilities of different structural isomers may be rationalized simply with recourse to π-Hückel theory. However, upon a greater degree of functionalization, π-electronic effects alone are incapable of describing the interaction between the functional groups and the distorted cage, and both σ- and π-electronic structure must be taken into account in order to understand the relative isomer stabilities.

Structural systematics and conformational analyses of a 3 × 3 isomer grid of fluoro-N-(pyridyl)benzamides: physicochemical correlations, polymorphism and isomorphous relationships

An isomer grid of nine fluoro-N-(pyridyl)benzamides (Fxx) (x = para-/meta-/ortho-) has been examined to correlate structural relationships between the experimental crystal structure and ab initio calculations, based on the effect of fluorine (Fx) and pyridine N-atom (x) substitution patterns on molecular conformation. Eight isomers form N-H⋅⋅⋅N hydrogen bonds, and only one (Fom) aggregates via intermolecular N-H⋅⋅⋅O=C interactions exclusively. The Fpm and Fom isomers both crystallize as two polymorphs with Fpm_O (N-H⋅⋅⋅O=C chains, P-syn) and Fpm_N (N-H⋅⋅⋅N chains, P-anti) both in P2(1)/n (Z' = 1) differing by their meta-N atom locations (P-syn, P-anti; N(pyridine) referenced to N-H), whereas the disordered Fom_O is mostly P-syn (Z' = 6) compared with Fom_F (P-anti) (Z' = 1). In the Fxo triad twisted dimers form cyclic R(2)(2)(8) rings via N-H⋅⋅⋅N interactions. Computational modelling and conformational preferences of the isomer grid demonstrate that the solid-state conformations generally conform with the most stable calculated conformations except for the Fxm triad, while calculations of the Fox triad predict the intramolecular N-H⋅⋅⋅F interaction established by spectroscopic and crystallographic data. Comparisons of Fxx with related isomer grids reveal a high degree of similarity in solid-state aggregation and physicochemical properties, while correlation of the melting point behaviour indicates the significance of the substituent position on melting point behaviour rather than the nature of the substituent.

Degradation of erythromycin in honey and selection of suitable marker residues for food safety analysis

Abstract Extra-label use of veterinary medications in apiculture is a practice which is known to result in the presence of drug residues in honey. Erythromycin has been used by some beekeepers in an attempt to control foulbrood diseases in honey bees. It is recognised that erythromycin degrades in acidic aqueous solutions to yield predominantly anhydroerythromycin. Honey is an acidic medium in which erythromycin should also degrade. Three degradation products with a molecular weight of 715 Da (anhydroerythromycin, erythromycin enol ether, and an unidentified but suspected related isomer) have been confirmed to be formed in honey. Erythromycin was found to degrade rapidly in honey at typical hive temperature with a half-life of less than one day. Based on these results, it is recommended that food safety laboratories include degradation products in analytical testing protocols when examining honey for erythromycin residues.

Pallambins A and B, Unprecedented Hexacyclic 19-nor-Secolabdane Diterpenoids from the Chinese Liverwort Pallavicinia ambigua

Pallambins A (1) and B (2), two novel 19-nor-7,8-secolabdane diterpenoids with unprecedented tetracyclo[4.4.0(3,5).0(2,8)]decane skeletons, along with a pair of structurally related isomers, pallambins C (3) and D (4), were isolated from the Chinese liverwort Pallavicinia ambigua. Their structures with absolute configurations were determined by means of NMR, X-ray diffraction, and CD analyses. Their preliminary cytotoxicity to human cancer cells was also tested.

Relative Isomer Abundance of Fullerenes and Carbon Nanotubes Correlates with Kinetic Stability

A methodology to evaluate the kinetic stability of carbon nanostructures is presented based on the assumption of the independent and random nature of thermal vibrations. The kinetic stability is directly correlated to the cleavage probability for the weakest bond of a given nanostructure. The application of the presented method to fullerenes and carbon nanotubes yields clear correlation to their experimentally observed relative isomer abundances. The general and simple formulation of the method ensures its applicability to other nanostructures for which formation is controlled by kinetic factors.

Differentiation of Closely Related Isomers: Application of Data Mining Techniques in Conjunction with Variable Wavelength Infrared Multiple Photon Dissociation Mass Spectrometry for Identification of Glucose-Containing Disaccharide Ions

Data mining algorithms have been used to analyze the infrared multiple photon dissociation (IRMPD) patterns of gas-phase lithiated disaccharide isomers irradiated with either a line-tunable CO(2) laser or a free electron laser (FEL). The IR fragmentation patterns over the wavelength range of 9.2-10.6 μm have been shown in earlier work to correlate uniquely with the asymmetry at the anomeric carbon in each disaccharide. Application of data mining approaches for data analysis allowed unambiguous determination of the anomeric carbon configurations for each disaccharide isomer pair using fragmentation data at a single wavelength. In addition, the linkage positions were easily assigned. This combination of wavelength-selective IRMPD and data mining offers a powerful and convenient tool for differentiation of structurally closely related isomers, including those of gas-phase carbohydrate complexes.

ChemInform Abstract: Synthesis, Structure, and Behavior in Solution of the Dawson Thio Derivative [(P2W17O61)2 (H4Mo4S4O6)]16‐.

AbstractHydrolysis of (NMe4)xK2‐x [I2Mo10S10O10(OH)10 (H2O)5] with 0.3 M aq.

Azide derivatized anticancer agents of Vitamin K3: X-ray structural, DSC, resonance spectral and API studies

Abstract Compound 1 [1-imino (acetyl hydrazino)–Vitamin K 3 ], displays valence tautomerically related electronic isomers as Form I and Form II . Form I exhibits 2D packing fragment with 1D ribbon chains of N–H⋯O hydrogen bonds and shows EPR silent features. While Form II is EPR active and exhibits biradical nature with double quantum transitions at g = 2.0040. 1 H NMR of compound 2 , [1-imino (hydrazino carboxylate)–Vitamin K 3 ] and Form II exhibit π delocalization via resonance assisted H-bonding [RAHB] effect compared to Form I . Molecular interactions in Form I and II are visualized by DSC. The electronic structures of compounds 1 and 2 have been correlated to their API values by measuring anticancer activities, mitochondrial potentials and DNA shearing patterns. Form II and compound 2 indicate mitochondria mediated apoptosis (∼75% cell death) while Form I causes 35% cell death.

Synthesis, Structure, and Behavior in Solution of the Dawson Thio Derivative [(P2W17O61)2(H4Mo4S4O6)]16–

AbstractThe [(P4W34O61)2{Mo4S4O4(OH2)2}]16– anion was obtained by the stereospecific addition of the [Mo2S2O2]2+ oxothio cation to the monovacant α2‐[P2W17O61]10– anion. The mixed salt K9Na7[(P2W17O61)2{Mo4S4O4(OH2)2}]·50H2O was isolated as single crystals and characterized by X‐ray diffraction. The analysis reveals that the anion adopts a “sandwich‐like” dimeric structure in which the two α2‐[P2W17O61]10– subunits are assembled in a transoid disposition with respect to the central cluster {H4Mo4S4O6}. In aqueous solution, an isomerization process is evidenced by 31P NMR spectroscopy and interpreted as the formation of the related cisoid isomer. A ratio of 30:70 of the transoid and cisoid isomers was found at equilibrium. The kinetic constants and activation parameters of the isomerization process were determined by variable‐temperature 31P NMR experiments. At 303 K, the process was slow (t1/2 = 160 min). The activation parameters are discussed with regard to a possible isomerization mechanism.

Isomer Population Analysis of Gaseous Ions From Infrared Multiple Photon Dissociation Kinetics

Infrared multiple photon dissociation (IRMPD) kinetics measured with tunable laser radiation from a free electron laser (FEL) are used to probe the relative populations of and interconversions between energetically competitive isomers of gas-phase ions at 298 K. On-resonance IRMPD kinetics of monoisomeric benzoate anion and anilinium (protonated aniline) are measured to determine the extent of overlap of the laser beam with the precursor ion population (∼93%). IRMPD kinetics indicating different photodissociation behavior for different isomers obtained at isomer-specific resonances are used to determine relative populations of salt bridge and charge-solvated isomers for ArgGly·Na(+), Ser·Cs(+), and Arg·Na(+). These values and Gibbs free energy differences obtained from them for thermal precursor populations are compared to values reported using other, less direct population probes. Rapid interconversion of two charge-solvated isomers occurs for ArgGly·Li(+), precluding population analysis for this ion. ArgGly·Na(+), ArgGly·Li(+), and Arg·Na(+) exhibit IRMPD induction periods lasting many seconds for some isomers at the laser photon energies and power used, indicating that IRMPD relative spectral intensities are time-dependent for these ions and that the relative band intensities in IRMPD spectra measured with short irradiation times may not provide meaningful information about relative isomer populations. These results constitute the first direct probe of ion isomer populations using IRMPD kinetics obtained with a FEL and illustrate a number of caveats in interpreting IRMPD spectra measured with just a single irradiation time. These results also indicate that more complete overlap of the laser beam with the ions will be highly advantageous in future instrument designs for IRMPD kinetics and spectroscopy experiments.

A comparison of methods for the measurement of 8-isoPGF2α: a marker of oxidative stress

Oxidative stress describes the cellular damage caused by excess reactive oxygen species not adequately inactivated by antioxidants. Oxidative stress has been implicated in playing a role in many disorders. Lipid peroxidation end-products are employed as markers of oxidative stress, of which the isoprostane, 8-iso-PGF(2α), is widely used. 8-iso-PGF(2α) is measured in plasma or urine by gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectrometry (LC/MS), tandem-mass spectrometry or enzyme-linked immunosorbent assay (ELISA). However, discrepancies between the specificity of these methods means correlation is poor. A tandem-mass spectrometric (LC/MS/MS) method, using immunoaffinity purification, for urinary 8-iso-PGF(2α) was developed and compared with two commercial ELISAs (A--Cayman Chemicals, B--Oxford Biomedical Research) in urine samples (n = 156). An LC/MS/MS method coupled to immunoaffinity purification was developed with satisfactory performance and comparison to ELISAs A and B. Spearman rank correlation demonstrated significant correlation between all methods (P = <0.0001); however, r² values ranged from 0.68 to 0.72. Bland-Altman plots revealed a proportional positive bias of ELISA B when compared with ELISA A and LC/MS/MS. Furthermore, the agreement between ELISA A and LC/MS/MS was poor. The poor agreement between methods for measurement of 8-iso-PGF(2α) highlights differences in selectivity. 8-iso-PGF(2α) is an isoprostane, a family of isomeric end-products of arachidonic acid peroxidation, which are produced by peroxidation or enzymatically. This makes avoiding cross-reactivity between 8-iso-PGF(2α) and related isomers challenging. When assessing oxidative stress studies, the selectivity of the methods used should be taken into account, particularly when comparing studies.