Semiconducting and Metallic [5,5] Fullertube Nanowires: Characterization of Pristine D5h(1)-C90 and D5d(1)-C100.

Although fullerenes were discovered nearly 35 years ago, scientists still struggle to isolate "single molecule" tubular fullerenes larger than C90. In similar fashion, there is a paucity of reports for pristine single-walled carbon nanotubes (SWNTs). In spite of Herculean efforts, the isolation and properties of pristine members of these carbonaceous classes remain largely unfulfilled. For example, the low abundance of spherical and tubular higher fullerenes in electric-arc extracts (<0.01-0.5%) and multiplicity of structural isomers remain a major challenge. Recently, a new isolation protocol for highly tubular fullerenes, also called f ullertubes, was reported. Herein, we describe spectroscopic characterization including 13C NMR, XPS, and Raman results for purified [5,5] fullertube family members, D5h-C90 and D5d-C100. In addition, DFT computational HOMO-LUMO gaps, polarizability indices, and electron density maps were also obtained. The Raman and 13C NMR results are consistent with semiconducting and metallic properties for D5h-C90 and D5d-C100, respectively. Our report suggests that short [5,5] fullertubes with aspect ratios of only ∼1.5-2 are metallic and could exhibit unique electronic properties.

Antiplasmodial Chromanes and Chromenes from the Monotypic Plant Species Koeberlinia spinosa.

Nine new compounds containing either a chromane or chromene ring moiety were isolated from the monotypic plant Koeberlinia spinosa. Compounds 1-4 are chromanes with all possible E and Z isomers of the isoprenoid side chain, with compound 5 a methylated derivative of 1. Compounds 6 and 7 were assigned as diastereomeric cyclized derivatives of 2 and were probably artifacts formed during the extraction or the isolation processes. Compounds 8 and 9 were characterized as new chromenes. Structure elucidation of 1-9 was conducted via 1D and 2D NMR spectroscopic data interpretation, and absolute configurations were determined by ECD spectroscopic analysis. Compounds 2, 5, 6, and 7 had weak antiplasmodial activity, while none of the compounds exhibited antiproliferative activity. The isolation, structure elucidation, and biological evaluation of these compounds are presented.

Recent Advances in Sequence-Controlled Ring-Opening Copolymerizations of Monomer Mixtures.

Transforming renewable resources into functional and degradable polymers is driven by the ever-increasing demand to replace unsustainable polyolefins. However, the utility of many degradable homopolymers remains limited due to their inferior properties compared to commodity polyolefins. Therefore, the synthesis of sequence-defined copolymers from one-pot monomer mixtures is not only conceptually appealing in chemistry, but also economically attractive by maximizing materials usage and improving polymers' performances. Among many polymerization strategies, ring-opening (co)polymerization of cyclic monomers enables efficient access to degradable polymers with high control on molecular weights and molecular weight distributions. Herein, we highlight recent advances in achieving one-pot, sequence-controlled polymerizations of cyclic monomer mixtures using a single catalytic system that combines multiple catalytic cycles. The scopes of cyclic monomers, catalysts, and polymerization mechanisms are presented for this type of sequence-controlled ring-opening copolymerization.

Isotope enhanced approaches in metabolomics.

The rapidly growing area of "metabolomics," in which a large number of metabolites from body fluids, cells or tissue are detected quantitatively, in a single step, promises immense potential for a number of disciplines including early disease diagnosis, therapy monitoring, systems biology, drug discovery and nutritional science. Because of its ability to detect a large number of metabolites in intact biological samples reproducibly and quantitatively, nuclear magnetic resonance (NMR) spectroscopy has emerged as one of the most powerful analytical techniques in metabolomics. NMR spectroscopy of biological samples with isotope labeling of metabolites using nuclei such as (2)H, (13)C, (15)N and (31)P, either in vivo or ex vivo, has dramatically improved our ability to identify low concentrated metabolites and trace important metabolic pathways. Considering the somewhat limited sensitivity and high complexity of NMR spectra of biological samples, efforts have been made to increase sensitivity and selectivity through isotope labeling methods, which pave novel avenues to unravel biological complexity and understand cellular functions in health and various disease conditions. This chapter describes current developments in isotope labeling of metabolites in vivo as well as ex vivo, and their potential metabolomics applications.

Backbone 1H, 15N, and 13C resonance assignments of the Phafin2 pleckstrin homology domain.

Phafin2 is a peripheral protein that triggers cellular signaling from endosomal and lysosomal compartments. The specific subcellular localization of Phafin2 is mediated by the presence of a tandem of phosphatidylinositol 3-phosphate (PtdIns3P)-binding domains, the pleckstrin homology (PH) and the Fab-1, YOTB, Vac1, and EEA1 (FYVE) domains. The requirement for both domains for binding to PtdIns3P still remains unclear. To understand the molecular interactions of the Phafin2 PH domain in detail, we report its nearly complete 1H, 15N, and 13C backbone resonance assignments.

Solvent manipulation of the pre-reduction metal-ligand complex and particle-ligand binding for controlled synthesis of Pd nanoparticles.

Understanding how to control the nucleation and growth rates is crucial for designing nanoparticles with specific sizes and shapes. In this study, we show that the nucleation and growth rates are correlated with the thermodynamics of metal-ligand/solvent binding for the pre-reduction complex and the surface of the nanoparticle, respectively. To obtain these correlations, we measured the nucleation and growth rates by in situ small angle X-ray scattering during the synthesis of colloidal Pd nanoparticles in the presence of trioctylphosphine in solvents of varying coordinating ability. The results show that the nucleation rate decreased, while the growth rate increased in the following order, toluene, piperidine, 3,4-lutidine and pyridine, leading to a large increase in the final nanoparticle size (from 1.4 nm in toluene to 5.0 nm in pyridine). Using density functional theory (DFT), complemented by 31P nuclear magnetic resonance and X-ray absorption spectroscopy, we calculated the reduction Gibbs free energies of the solvent-dependent dominant pre-reduction complex and the solvent-nanoparticle binding energy. The results indicate that lower nucleation rates originate from solvent coordination which stabilizes the pre-reduction complex and increases its reduction free energy. At the same time, DFT calculations suggest that the solvent coordination affects the effective capping of the surface where stronger binding solvents slow the nanoparticle growth by lowering the number of active sites (not already bound by trioctylphosphine). The findings represent a promising advancement towards understanding the microscopic connection between the metal-ligand thermodynamic interactions and the kinetics of nucleation and growth to control the size of colloidal metal nanoparticles.

Quantitative analysis of blood plasma metabolites using isotope enhanced NMR methods.

NMR spectroscopy is a powerful analytical tool for both qualitative and quantitative analysis. However, accurate quantitative analysis in complex fluids such as human blood plasma is challenging, and analysis using one-dimensional NMR is limited by signal overlap. It is impractical to use heteronuclear experiments involving natural abundance (13)C on a routine basis due to low sensitivity, despite their improved resolution. Focusing on circumventing such bottlenecks, this study demonstrates the utility of a combination of isotope enhanced NMR experiments to analyze metabolites in human blood plasma. (1)H-(15)N HSQC and (1)H-(13)C HSQC experiments on the isotope tagged samples combined with the conventional (1)H one-dimensional and (1)H-(1)H TOCSY experiments provide quantitative information on a large number of metabolites in plasma. The methods were first tested on a mixture of 28 synthetic analogues of metabolites commonly present in human blood; 27 metabolites in a standard NIST (National Institute of Standards and Technology) human blood plasma were then identified and quantified with an average coefficient of variation of 2.4% for 17 metabolites and 5.6% when all the metabolites were considered. Carboxylic acids and amines represent a majority of the metabolites in body fluids, and their analysis by isotope tagging enables a significant enhancement of the metabolic pool for biomarker discovery applications. Improved sensitivity and resolution of NMR experiments imparted by (15)N and (13)C isotope tagging are attractive for both the enhancement of the detectable metabolic pool and accurate analysis of plasma metabolites. The approach can be easily extended to many additional metabolites in almost any biological mixture.

Chemoselective 15N tag for sensitive and high-resolution nuclear magnetic resonance profiling of the carboxyl-containing metabolome.

Metabolic profiling has received increasing recognition as an indispensable complement to genomics and proteomics for probing biological systems and for clinical applications. (1)H nuclear magnetic resonance (NMR) is widely used in the field but is challenged by spectral complexity and overlap. Improved and simple methods that quantitatively profile a large number of metabolites are sought to make further progress. Here, we demonstrate a simple isotope tagging strategy, in which metabolites with carboxyl groups are chemically tagged with (15)N-ethanolamine and detected using a 2D heteronuclear correlation NMR experiment. This method is capable of detecting over 100 metabolites at concentrations as low as a few micromolar in biological samples, both quantitatively and reproducibly. Carboxyl-containing compounds are found in almost all metabolic pathways, and thus this new approach should find a variety of applications.

1H NMR metabolomics study of age profiling in children.

Metabolic profiling of urine provides a fingerprint of personalized endogenous metabolite markers that correlate to a number of factors such as gender, disease, diet, toxicity, medication, and age. It is important to study these factors individually, if possible to unravel their unique contributions. In this study, age-related metabolic changes in children of age 12 years and below were analyzed by (1)H NMR spectroscopy of urine. The effect of age on the urinary metabolite profile was observed as a distinct age-dependent clustering even from the unsupervised principal component analysis. Further analysis, using partial least squares with orthogonal signal correction regression with respect to age, resulted in the identification of an age-related metabolic profile. Metabolites that correlated with age included creatinine, creatine, glycine, betaine/TMAO, citrate, succinate, and acetone. Although creatinine increased with age, all the other metabolites decreased. These results may be potentially useful in assessing the biological age (as opposed to chronological) of young humans as well as in providing a deeper understanding of the confounding factors in the application of metabolomics.

Visualization of bile homeostasis using (1)H-NMR spectroscopy as a route for assessing liver cancer.

Changes in bile synthesis by the liver or alterations in the enterohepatic circulation due to a variety of etiological conditions may represent a novel source of liver disease-specific biomarkers. Bile from patients with liver diseases exhibited significant changes in the levels of glycine- and taurine-conjugated bile acids, phospholipids, cholesterol and urea relative to non-liver disease controls. Cholangiocarcinoma and non-malignant liver diseases (NMLD) showed the most significant alterations. Further, hepatocellular carcinoma (HCC) could be differentiated from NMLD (p = 0.02), as well as non-liver disease controls (p = 0.02) based on the amounts of bile acids, phospholipids and/or cholesterol. HCC also differed with cholangiocarcinoma although not significantly. Urea increases somewhat in non-malignant liver disease relative to non-liver disease controls, while the bile acids, phospholipids and cholesterol all decrease significantly. The ratio between some major bile metabolites also distinguished NMLD (p = 0.004-0.01) from non-liver disease controls. This snapshot view of bile homeostasis, is obtainable from a simple nuclear magnetic resonance (NMR) approach and demonstrates the enormous opportunity to assess liver status, explore biomarkers for high risk diseases such as cancers and improve the understanding of normal and abnormal cellular functions.

Application of 31P NMR spectroscopy and chemical derivatization for metabolite profiling of lipophilic compounds in human serum.

New methods for obtaining metabolic fingerprints of biological samples with improved resolution and sensitivity are highly sought for early disease detection, studies of human health and pathophysiology, and for better understanding systems biology. Considering the complexity of biological samples, interest in biochemical class selection through the use of chemoselective probes for improved resolution and quantitation is increasing. Considering the role of lipids in the pathogenesis of a number of diseases, in this study fingerprinting of lipid metabolites was achieved by (31)P labeling using the derivatizing agent 2-chloro-4,4,5,5-tetramethyldioxaphospholane. Lipids containing hydroxyl, aldehyde and carboxyl groups were selectively tagged with (31)P and then detected with good resolution using (31)P NMR by exploiting the 100% natural abundance and wide chemical shift range of (31)P. After standardizing the reaction conditions using representative compounds, the derivatization approach was used to profile lipids in human serum. The results show that the (31)P derivatization approach is simple, reproducible and highly quantitative, and has the potential to profile a number of important lipids in complex biological samples.

Correlative and quantitative 1H NMR-based metabolomics reveals specific metabolic pathway disturbances in diabetic rats.

Type 1 diabetes was induced in Sprague-Dawley rats using streptozotocin. Rat urine samples (8 diabetic and 10 control) were analyzed by 1H nuclear magnetic resonance (NMR) spectroscopy. The derived metabolites using univariate and multivariate statistical analysis were subjected to correlative analysis. Plasma metabolites were measured by a series of bioassays. A total of 17 urinary metabolites were identified in the 1H NMR spectra and the loadings plots after principal components analysis. Diabetic rats showed significantly increased levels of glucose (P < 0.00001), alanine (P < 0.0002), lactate (P < 0.05), ethanol (P < 0.05), acetate (P < 0.05), and fumarate (P < 0.05) compared with controls. Plasma assays showed higher amounts of glucose, urea, triglycerides, and thiobarbituric acid-reacting substances in diabetic rats. Striking differences in the Pearson's correlation of the 17 NMR-detected metabolites were observed between control and diabetic rats. Detailed analysis of the altered metabolite levels and their correlations indicate a significant disturbance in the glucose metabolism and tricarboxylic acid (TCA) cycle and a contribution from gut microbial metabolism. Specific perturbed metabolic pathways include the glucose-alanine and Cori cycles, the acetate switch, and choline metabolism. Detection of the altered metabolic pathways and bacterial metabolites using this correlative and quantitative NMR-based metabolomics approach should help to further the understanding of diabetes-related mechanisms.

Ibuprofen metabolite profiling using a combination of SPE/column-trapping and HPLC-micro-coil NMR.

Solid-phase extraction and column-trapping preconcentration are combined to enhance HPLC-nuclear magnetic resonance (HPLC-NMR) and applied to metabolite profiling in biological samples. Combining the two signal enhancement techniques improved the NMR signal substantially such that we were able to identify 2-hydroxyibuprofen, carboxyibuprofen, and unmetabolized ibuprofen molecules from a small urine sample after a therapeutic dose of ibuprofen. The hyphenated SPE/column-trapping method resulted in an excellent overall signal enhancement of up to 90-fold.

Backbone 1H, 15N, and 13C resonance assignments of the Tom1 VHS domain.

Efficient trafficking of ubiquitinated receptors (cargo) to endosomes requires the recruitment of adaptor proteins that exhibit ubiquitin-binding domains for recognition and transport. Tom1 is an adaptor protein that not only associates with ubiquitinated cargo but also represents a phosphoinositide effector during specific bacterial infections. This phosphoinositide-binding property is associated with its N-terminal Vps27, Hrs, STAM (VHS) domain. Despite its biological relevance, there are no resonance assignments of Tom1 VHS available that can fully characterize its molecular interactions. Here, we report the nearly complete 1H, 15N, and 13C backbone resonance assignments of the VHS domain of human Tom1.

Subtleties of human exposure and response to chemical mixtures from spills.

Worldwide, chemical spills degrade drinking water quality and threaten human health through ingestion and inhalation. Spills are often mixtures of chemicals; thus, understanding the interaction of chemical and biological properties of the major and minor components is critical to assessing human exposure. The crude (4-methylcyclohexyl)methanol (MCHM) spill provides an opportunity to assess such subtleties. This research determined the relative amounts, volatilization, and biological odor properties of minor components cis- and trans-methyl-4-methylcyclohexanecarboxylate (MMCHC) isomers and major components cis- and trans-4-MCHM, then compared properties and human exposure differences among them. (1)H nuclear magnetic resonance and chromatography revealed that the minor MMCHC isomers were about 1% of the major MCHM isomers. At typical showering temperature of 40 °C, Henry's law constants were 1.50 × 10(-2) and 2.23 × 10(-2) for cis- and trans-MMCHC, respectively, which is 20-50 fold higher than for 4-MCHM isomers. The odor thresholds were 1.83 and 0.02 ppb-v air for cis- and trans-MMCHC, which were both described as predominantly sweet. These data are compared to the higher 120 ppb-v air and 0.06 ppb-v odor thresholds for cis- and trans-4-MCHM, for which the trans-isomer had a dominant licorice descriptor. Application of a shower model demonstrated that while MMCHC isomers are only about 1% of the MCHM isomers, during showering, the MMCHC isomers are 13.8% by volume (16.3% by mass) because of their higher volatility. Trans-4-MCHM contributed about 82% of the odor because of higher volatility and lower odor threshold, trans-MMCHC, which represents 0.3% of the mass, contributed 18% of the odor. This study, with its unique human sensory component to assess exposure, reaffirmed that hazard assessment must not be based solely on relative concentration, but also consider the chemical fate, transport, and biological properties to determine the actual levels of exposure across different media.

Identification and characterization of phenylacetonitrile as a nitrogenous disinfection byproduct derived from chlorination of phenylalanine in drinking water.

Unregulated disinfection byproducts (DBPs), including nitrogenous disinfection byproducts (N-DBPs), originating from chlorination of the precursor amino acid phenylalanine in aqueous systems, were identified in laboratory reactions and distributed tap. The major N-DBP identified was phenylacetonitrile, and minor DBPs of benzyl chloride, phenylacetaldehyde, 2-chlorobenzyl cyanide, and 2, 6-diphenylpyridine were also formed. Phenylacetonitrile was generated through decarboxylation, dechlorination and/or hydrolysis processes. With an aromatic structure, phenylacetonitrile has an unpleasant odor of various descriptors and an odor threshold concentration of 0.2 ppt-v as measured through gas chromatography-olfactometry. The half-life of phenylacetonitrile in reagent water and chlorinated water at 19 °C were 121 h and 792 h, respectively. The occurrence of phenylacetonitrile as an N-DBP in tap water was investigated for the first time; the results revealed that µg/L concentrations were present in nine different distributed drinking waters in China and the United States. Phenylacetonitrile deteriorates the aesthetic quality of drinking water and may present risk due to its prolonged existence in drinking water, especially in the presence of residual chlorine.

Early detection of recurrent breast cancer using metabolite profiling.

We report on the development of a monitoring test for recurrent breast cancer, using metabolite-profiling methods. Using a combination of nuclear magnetic resonance (NMR) and two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) methods, we analyzed the metabolite profiles of 257 retrospective serial serum samples from 56 previously diagnosed and surgically treated breast cancer patients. One hundred sixteen of the serial samples were from 20 patients with recurrent breast cancer, and 141 samples were from 36 patients with no clinical evidence of the disease during ∼6 years of sample collection. NMR and GC×GC-MS data were analyzed by multivariate statistical methods to compare identified metabolite signals between the recurrence samples and those with no evidence of disease. Eleven metabolite markers (seven from NMR and four from GC×GC-MS) were shortlisted from an analysis of all patient samples by using logistic regression and 5-fold cross-validation. A partial least squares discriminant analysis model built using these markers with leave-one-out cross-validation provided a sensitivity of 86% and a specificity of 84% (area under the receiver operating characteristic curve = 0.88). Strikingly, 55% of the patients could be correctly predicted to have recurrence 13 months (on average) before the recurrence was clinically diagnosed, representing a large improvement over the current breast cancer-monitoring assay CA 27.29. To the best of our knowledge, this is the first study to develop and prevalidate a prediction model for early detection of recurrent breast cancer based on metabolic profiles. In particular, the combination of two advanced analytical methods, NMR and MS, provides a powerful approach for the early detection of recurrent breast cancer.

Combining nuclear magnetic resonance spectroscopy and mass spectrometry in biomarker discovery.

Metabolic profiling of biological specimens is emerging as a promising approach for discovering specific biomarkers in the diagnosis of a number of diseases. Amongst many analytical techniques, nuclear magnetic resonance spectroscopy and mass spectrometry are the most information-rich tools that enable high-throughput and global analysis of hundreds of metabolites in a single step. Although only one of the two techniques is utilized in a majority of metabolomics applications, there is a growing interest in combining the data from the two methods to effectively unravel the mammoth complexity of biological samples. In this article, current developments in nuclear magnetic resonance, mass spectrometry and multivariate statistical analysis methods are described. While some general applications that utilize the combination of the two analytical methods are presented briefly, the emphasis is laid on the recent applications of nuclear magnetic resonance and mass spectrometry methods in the studies of hepatopancreatobiliary and gastrointestinal malignancies.

Bile acids conjugation in human bile is not random: new insights from (1)H-NMR spectroscopy at 800 MHz.

Bile acids constitute a group of structurally closely related molecules and represent the most abundant constituents of human bile. Investigations of bile acids have garnered increased interest owing to their recently discovered additional biological functions including their role as signaling molecules that govern glucose, fat and energy metabolism. Recent NMR methodological developments have enabled single-step analysis of several highly abundant and common glycine- and taurine- conjugated bile acids, such as glycocholic acid, glycodeoxycholic acid, glycochenodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, and taurochenodeoxycholic acid. Investigation of these conjugated bile acids in human bile employing high field (800 MHz) (1)H-NMR spectroscopy reveals that the ratios between two glycine-conjugated bile acids and their taurine counterparts correlate positively (R2 = 0.83-0.97; p = 0.001 x 10(-2)-0.006 x 10(-7)) as do the ratios between a glycine-conjugated bile acid and its taurine counterpart (R2 = 0.92-0.95; p = 0.004 x 10(-3)-0.002 x 10(-10)). Using such correlations, concentration of individual bile acids in each sample could be predicted in good agreement with the experimentally determined values. These insights into the pattern of bile acid conjugation in human bile between glycine and taurine promise useful clues to the mechanism of bile acids' biosynthesis, conjugation and enterohepatic circulation, and may improve our understanding of the role of individual conjugated bile acids in health and disease.

Identification of 4-deoxythreonic acid present in human urine using HPLC and NMR techniques.

The 1H NMR spectrum of urine exhibits a large number of detectable and quantifiable metabolites and hence urine metabolite profiling is potentially useful for the study of systems biology and the discovery of biomarkers for drug development or clinical applications. While a number of metabolites (50-100) are readily detectable in urine by NMR, a much larger number is potentially available if lower concentration species can be detected unambiguously. Lower concentration metabolites are thought to be more specific to certain disease states and thus it is important to detect these metabolites with certainty. We report the identification of 4-deoxythreonic acid, a relatively low concentration endogenous metabolite that has not been previously identified in the 1H NMR spectrum of human urine. The use of HPLC and NMR spectroscopy facilitated the unequivocal and non-invasive identification of the molecule in urine which is complicated by extensive peak overlap and multiple, similar resonances from other metabolites such as 3-hydroxybutanoic acid. High-resolution detection and good sensitivity were achieved by the combination of multiple chromatographic fraction collection, sample pre-concentration, and the use of a cryogenically cooled NMR probe.