Application Of Spectroscopic Methods Research Articles

A New Eremophilane Sesquiterpene from Senecio Nemorensis

A new eremophilane sesquiterpene was isolated from the MeOH extract of the aerial parts of Senecio nemorensis. Its structure was established as 11-hydroxy-1β-methoxyl-8-oxoeremophila-6,9-dien-12-oic methyl ester by extensive application of spectroscopic methods, including IR, EI-MS, HR-ESI-MS, 1D and 2D NMR spectroscopy.

Time-resolved spectroscopy in study of the intramolecular vibrational dynamics: Recent results and future prospects

Applications of spectroscopic methods in real-time investigations of the vibrational energy redistribution in an isolated polyatomic molecule are reviewed. The results of the latest experiments with propyne and its derivatives according to the pump-probe scheme with the use of Raman spectroscopy are reported. The main result is the key role of the energy transfer between the vibrational and rotational degrees of freedom in the molecules studied.

Fourier Transform Infrared (FTIR) Spectroscopy of Biological Tissues

This article reviews some of the recent advances on FTIR spectroscopy in areas related to natural tissues and cell biology. It is the second review publication resulting from a detailed study on the applications of spectroscopic methods in biological studies and summarizes some of the most widely used peak frequencies and their assignments. The aim of these studies is to prepare a database of molecular fingerprints, which will help researchers in defining the chemical structure of the biological tissues introducing most of the important peaks present in the natural tissues. In spite of applying different methods, there seems to be a considerable similarity in defining the peaks of identical areas of the FTIR spectra. As a result, it is believed that preparing a unique collection of the frequencies encountered in FTIR spectroscopic studies can lead to significant improvements both in the quantity and quality of research and their outcomes. This article is the first review of its kind that provides a precise database on the most important FTIR characteristic peak frequencies for researchers aiming to analyze natural tissues by FTIR spectroscopy and will be of considerable assistance to those who are focusing on the analysis of cancerous tissues by FTIR spectroscopy.

Oxanthrone C-glycosides and epoxynaphthoquinol from the roots of Rumex japonicus

Five oxanthrone C-glycosides, namely rumejaposide A–E, and an epoxynaphthoquinol, together with eight known compounds, 2,6-dihydroxy benzoic acid, 4-hydroxy benzoic acid, epicatechin, 4-hydroxy-3-methoxy benzoic acid, 2,6-dimethoxy-4-hydroxyl benzoic acid, rutin, emodin and 2-acetyl-1,8-dihydroxy-3-methyl-6-methoxynaphthalene, were isolated from the roots of Rumex japonicus. The structures of the oxanthrone C-glycosides were elucidated by application of spectroscopic methods as (10 R)10- C-β-glucopyranosyl-1,8,10-trihydroxy-2-carboxyl-3-methyl-9(10 H)-anthracenone, (10 S)10- C-β-glucopyranosyl-1,8,10-trihydroxy-2-carboxyl-3-methyl-9(10 H)-anthracenone, (10 R)10- C-β-glucopyranosyl-1,6,8,10-tetrahydroxy-2-carboxyl-3-methyl-9(10 H)-anthracenone, (10 R)10- C-β-glucopyranosyl-1,6,8,10-tetrahydroxy-3-hydroxymethyl-9(10 H)-anthracenone, and (10 R)10- C-β-glucopyranosyl-1,6,8,10-tetrahydroxy-3-methyl-9(10 H)-anthracenone. Absolute configurations for each compound were deduced by analyses of CD spectra and comparison with those known similar compounds. The structure of epoxynaphthoquinol was elucidated by spectroscopic methods as 3-acetyl-2-methyl-1,4,5-trihydroxy-2,3-epoxynaphthoquinol, and its relative configuration was determined by a 2D-ROESY experiment.

Investigating the Location of Propyl Gallate at Surfaces and Its Chemical Microenvironment by 1H NMR

The location and the resulting chemical microenvironment of the antioxidant propyl gallate (PG) was studied in micellar solutions using the cationic emulsifier cetyl trimethyl ammonium bromide (CTAB), the anionic emulsifier sodium dodecyl sulphate (SDS) and the non-ionic emulsifier Brij 58 (polyoxyethylene-20-cetyl ester). T (1) relaxation time of the aromatic protons of PG was investigated in micellar solutions and compared with that in aqueous solution in the absence of emulsifier. The relaxation time of the PG portion that is solubilized in the micelle (T (1,eff)) was calculated from the partition behavior of PG in micellar solution. From the 1D-(1)H spectrum, the alteration in the electron density of the aromatic protons and the alteration in the peak shape of the emulsifier headgroup and alkyl chain proton signals were indicative of the location of propyl gallate in the different micelles. Nuclear Overhauser effects (NOE) made it possible to deduce the exact location of PG by calculation of the relative NOEs. Marked differences were found for the location of PG in CTAB, SDS and Brij 58 micelles. PG was found to be located in the palisade layer of CTAB micelles, in the region of the polyoxyethylene chain of Brij micelles and in the Stern layer of SDS micelles. For careful study of the location of antioxidants and therefore to be able to characterize the chemical microenvironment of the antioxidants is crucial for understanding differences in antioxidant activities as a function of lipid surfaces. The application of spectroscopic methods may help to optimize the antioxidant activity to inhibit lipid oxidation at surfaces that are formed in a wide range of foods (emulsions), cosmetics, pharmaceuticals (emulsions and carrier systems) and of biological membranes (LDL-particles).

Study of the complexation of different methacrylates with cyclodextrins employing a combination of electrophoretic, chromatographic, and NMR‐spectroscopic methods

The present study describes the application of capillary electromigration techniques; CEC and micellar EKC (MEKC), and the application of spectroscopic methods; 1H NMR and 1H NOESY spectroscopy to investigate interactions between CDs (alpha-CD, statistically methylated beta-CD, hydroxypropyl-beta-CD, and 2-hydroxypropyl-gamma-CD) and different methacrylates (adamantyl, isobornyl, cyclohexyl, and phenyl methacrylate). It is shown that these methods complement each other. While CD-mediated MEKC is a rapid screening technique for comparing complex stabilities in aqueous media, 1H NMR chemical shift analysis provides quantitative data for very strong methacrylate-CD complexes and CD-mediated CEC provides quantitative data for complexes with lower complex forming constants. CD-mediated MEKC did not prove to be suitable for the calculation of complex forming constants. Reasons are discussed. 1H NOESY spectra were used to study spatial relationships between host and guest atoms.

Oxidative coupling of the pyrogallol B-ring with a galloyl group during enzymatic oxidation of epigallocatechin 3- O-gallate

In order to clarify the mechanism for formation of catechin oligomers during the fermentation stage of black tea manufacture, epigallocatechin-3- O-gallate, the most abundant tea flavanol in fresh tea leaves, was enzymatically oxidized and the resulting unstable quinone metabolites were converted to phenazine derivatives by treatment with o-phenylenediamine. In addition to formation of monomeric and dimeric derivatives, four trimeric derivatives were isolated whose structures were determined by application of spectroscopic methods. The derivatives differed from each other in the location of the phenazine moieties and in the atropisomerism of the biphenyl bond. The results suggested that oxidative coupling of the galloyl group with the B-ring proceeds by a quinone dimerization mechanism similar to that for production of theasinensins.

Preface

This special issue contains articles selected from those presented as lectures and posters at the 11th European Conference on the Spectroscopy of Biological Molecules (ECSBM 2005) held in Aschaffenburg, Germany, during September 3–8, 2005. This was the latest in the well-established ECSBM series of international conferences that are organized in alternate years in different European countries to provide a forum for the presentation and discussion of recent progress in the field of biomolecular spectroscopy. Further details on the 2005 meeting remain available on the conference web site at http://www.biophys.uni-frankfurt.de/ecsbmindex.html; the next conference in this series will take place in or near Paris, France, in September 2007. The issue contains 30 papers, all of which have been subject to the thorough review process that is given to any article to be published in Biopolymers. The subject matter covers a broad range of topics in the life sciences where the application of spectroscopic methods has yielded new insights into structure and/or function of the biomolecules studied. The articles are arranged in subsections concerned with biomedical systems and microorganisms (8 papers), structural studies (4), functional studies (6), biomolecules at surfaces (8), and theory/model compounds (4). The range of spectroscopic and other methods employed is similarly broad and encompasses both electronic and vibrational techniques, complemented by others such as atomic force microscopy (AFM), statistical analyses, computer modeling and ab initio molecular orbital (MO) calculations. The full set of articles represents well the state-of-the-art in this fast-moving field, which exploits the ever-increasing sophistication of spectroscopic methods to reveal new insights into both structure and dynamics of biomolecular systems. All of the articles were invited on the basis of a preconference selection from those offered to the organizers and all were rigorously reviewed by at least two referees. For the purpose of this publication, all of the articles were strictly page limited. One of us wishes to use this opportunity to acknowledge the hard work, initiative, and excellent organizational skills of the conference joint-chairmen, Professors Werner Maentele and Friedrich Siebert, and their hard-working local team drawn from their home universities of Frankfurt and Freiburg, respectively. The success of the conference was a tribute to all of them. We also are indeed grateful to all authors and referees for their cooperation and support, which has been essential in enabling us to prepare this issue for publication in a timely manner.

Characterization of Soil Organic Carbon in Long‐Term Amendment Trials

In the current study, total organic carbon (TOC) analysis and spectroscopic characterization (IRMS, DRIFT, and SERS) are applied to investigate the molecular changes in humic acids (HA) extracted from soil samples amended for more than 30 years with cattle manure (CM), cow slurries (CS), and crop residues (CR). All samples are compared to the unamended (T) sample. A variation in soil TOC percentage occurs in all samples, but a significant (P<0.05) accumulation of C is observed only in CM. The TOC δ 13C values appeared progressively less negative in all samples with respect to T. The DRIFT and SERS analyses of HA revealed a change in oxygenate groups (such as COO− and OH) in the amendment with CS and CR. These results suggest how amendment might affect both C accumulation and the HA structure. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Limitations of the Quantification of Organic Carbon in Sediment from C–H Stretching Vibrations in DRIFT Spectra

The limitations of quantifying organic carbon (OC) or various organic substances in sediment from the integration of infrared C–H stretching bands using diffuse reflectance infrared Fourier transform (DRIFT) spectra are pointed out, both from theoretical arguments and by presenting experimental data. Such determinations are inaccurate and imprecise because (i) the band at 2930 cm−1 is not exclusively due to CH2 groups; (ii) there is a spectral interference from CO3 2− absorption; and (iii) the proportion of CH2 groups in organic matter varies for different sediments. The measurement of aliphatic C–H stretching band areas only provides an approximate measurement of aliphatic carbon bonded to hydrogen, which turns out to be a factor of about 3 to 3.5 times smaller than the OC content for Hong Kong marine sediments, depending on their nature and origin. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Surface Plasmon Resonance‐Based Immunoassay for the Detection of Aflatoxin B1 Using Single‐Chain Antibody Fragments

Aflatoxin B1 (AFB1) is a highly toxic secondary metabolite of the fungal species Aspergillus flavus and Aspergillus parasiticus produced under certain environmental conditions. The gene encoding an AFB1‐specific single‐chain fragment variable (scFv) was isolated from a pre‐immunized phage display library and used to express a monomeric and dimeric scFv, specific for AFB1, in Escherichia coli. The monomeric and dimeric scFv were then applied to the development of surface plasmon resonance‐based inhibition immunoassays for the detection of AFB1. Regeneration of the sensor surface, which consisted of a CM5 chip immobilized with an AFB1 derivative, was investigated and enabled at least 75 binding regeneration cycles. The inhibition assays developed had ranges of detection between 390 and 12,000 pg mL−1 (ppb) for the monomeric scFv and between 190 and 24,000 pg mL−1 (ppb) for the dimeric scFv, with coefficients of variation for the inter‐day variability studies ranging from 1.9–4.18% and 3–11.53%, respectively. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems”. The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Characterization of Mango Juice by High‐Resolution NMR, Hyphenated NMR, and Diffusion‐Ordered Spectroscopy

The application of nuclear magnetic resonance (NMR) spectroscopy, hyphenated NMR, and diffusion‐ordered spectroscopy (DOSY) to the characterization of mango juice, as an example of a complex food mixture, is described. The compositional changes taking place as a function of ripening were followed, and selected metabolites were quantified by integration of the corresponding NMR peaks. In this way, an overall view of the metabolite changes is obtained, enabling the study of the biochemical mechanisms involved in the ripening process. More than 50 compounds were identified by 1D‐ and 2D‐NMR, but many ambiguous assignments remain due to spectral overlap or insufficient coupling information. The use of Liquid Chromatography (LC‐NMR) and LC‐NMR/Mass Spectrometry (MS) enables a fuller characterization of the soluble pectin fraction to be made; its dependence on ripening stage is discussed. Finally, DOSY adds information on the Mr of many metabolites, including the pectin fractions of ripe and unripe mango juices, and enables further peak assignments to be made. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Spectroscopic Analysis of Sequentially Extracted Humic Acid from Compost

Structural characterization of organic matter (OM) is crucial in assessing its role in soils and sediments. In this study, humic acids (HA) were sequentially extracted from a compost and characterized in terms of their molecular, chemical, and structural heterogeneity. HA was extracted in sequence a total of 28 times, using 0.1 mol L−1 Na4P2O7, and sequentially grouped into seven fractions. These fractions and the original compost were analyzed using UV–visible spectroscopy, 13C nuclear magnetic resonance spectroscopy (NMR), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and an elemental analyzer. 13C‐NMR and DRIFTS data indicated significant structural variations among the extracted HA fractions and the original compost. These data corresponded to a decrease in the atomic C/H ratio and to an increase in the atomic C/O ratio among these sequentially extracted HA fractions, which together represented an increase in aliphaticity in conjunction with a decrease in polarity and aromaticity. E4/E6 ratios indicated an increase in molecular size with increasing number of extractions. The structural variability of HA may significantly affect the sorption of organic pollutants and the reduction and complexation of metals by organic matter. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Nd:YAG Laser‐Based Photoacoustic Detection of Ozone: Comparison of Pulsed and Quasicontinuous Wave Operation and Field Tests

Sensitivity in the lower ppb range for ozone detection by a photoacoustic system based on a low repetition rate and a quasicontinuous wave (QCW) frequency quadrupled Nd:YAG laser system is demonstrated. The two systems were compared from various points of view such as available UV light power, minimum detectable ozone concentration, photoacoustic signal generation efficiency, as well as simplicity of construction and ease of operation. The QCW‐based system was found to have the potential in practical applications due to its relative simplicity and compactness. Therefore, after laboratory calibration it was tested at an environmental monitoring station: it was run in parallel with a routinely used ozone measuring instrument, where it showed reliable operation. #This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Real‐Time Monitoring of Transport of Chlorinated Hydrocarbons from Industrial Areas Using Open‐Path FTIR Spectrometry with COL1SB

Open‐path Fourier transform infrared (FTIR) spectrometry was used to continuously monitor 11 chlorinated hydrocarbon species in the region connecting two different industrial complexes for 24 hr. The single‐beam spectra obtained from open‐path FTIR were analyzed by newly developed software named COL1SB, which generates site‐specific background spectra as well as path‐averaged water vapor concentrations in addition to performing regression analyses. The path‐averaged water vapor concentrations calculated by the COL1SB agreed very well with those measured by a thermo‐hygrometer. In addition, site‐specific background spectra were generated by accounting for chemical absorption of 50 chemical species. The accurate estimation of path‐averaged water vapor concentrations, as well as the usage of site‐specific background spectra, enables chlorinated hydrocarbons to be measured by open‐path FTIR spectrometry at the ppb level. Among 11 chlorinated hydrocarbons considered here, trichlorofluoromethane, carbon tetrachloride, trichloroethylene, and tetrachloroethylene were identified as major chlorinated hydrocarbons having concentrations above 1 ppb. Wind affected the temporal variations of these chlorinated hydrocarbons, indicating the importance of local transport. However, the effect of wind differed from one species to another because of different source characteristics. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

The Use of Energy‐Dispersive X‐Ray Microanalysis as a Rapid Method for Demarcating Areas Around Marine Outfalls that may be Influenced by Effluent: A Case Study

Surveys that monitor pollution in a marine environment often include the measurement of heavy metals and other trace elements in sediments obtained from multiple stations near marine outfalls. This study investigates the use of energy‐dispersive x‐ray (EDX) microanalysis as a rapid screening method, where characteristic or “signature” elements (SE) in effluent can be located and mapped on the seabed. Thereafter, sediments from stations/areas with high SE can be examined using more sensitive spectroscopic methods, and, if present, trace metals quantified. To serve as controls, 21 samples of sediment were obtained from two “pristine” areas off the Kwazulu Natal coast. A further 99 samples were obtained from stations within 2 km of the Huntsman Tioxide pipeline. Each sample was sonicated to separate the coarse from fine fractions. The fines were collected on a paper filter and mounted next to its corresponding, washed, coarse fraction on a graphite stub. Each sample was coated with C and examined by EDX. Huntsman Tioxide effluent was rich in Ti and Fe. The fine and coarse fractions of all sediments were screened for these elements. A contamination index (I) was constructed from the combined fines, Ti and Fe data. Surfer 16 software was employed to create contour plots showing the distribution of Ti, Fe, and I in fine and Ti in coarse fractions of sediments near the Huntsman Tioxide pipeline. The results showed that EDX was an effective method for locating fallout “hot spots” and delimiting an area affected by effluent. #This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems.” The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Characterization of Individual Silicon‐Poor Particles in Atmospheric Aerosols by SEM‐EDX and Application to Kosa Particle Identification

Silicon‐poor particles, mainly composed of mafic minerals such as olivine or pyroxene, were examined as an indicator of eolian dust particles from China, called the Kosa aerosol in Japan. A method of scanning electron microscopy–energy dispersive x‐ray microanalysis (SEM‐EDX) has been developed to discriminate Kosa‐derived, individual Si‐poor particles from Japanese igneous rock–derived ones. Prior to single‐particle analysis by the SEM‐EDX, atmospheric particle samples were ignited at 1000°C for 6 hr, and thereafter the ignited samples were washed in hydrochloric acid, in order to remove organic matter, soluble‐formed secondary particles, easily‐weathering minerals having medium SiO2 content, and so forth. Particles having a SiO2 content of 30–50% in the residue after the acid treatment were defined as Si‐poor particles in this study, and the elemental composition was determined by SEM‐EDX using a standardless ϕ (ρz) correction. Si‐poor particles are characterized by their high contents of Mg and Fe, so that a correlation plot between MgO/Fe2O3 and MgO/SiO2 was examined for individual Si‐poor particles. Atmospheric aerosol sampling was carried out at the northern foot of Mt. Fuji, central Japan, and the distribution areas under the Kosa phenomena in the correlation plot widely differed from those of background aerosol at the sampling site. Also, the correlation plot showed a clear temporal variation corresponding to transporting episodes of the Kosa aerosol. The variation of major elements like Mg and Fe in Si‐poor particles was wide compared to that of trace impurities (Na and K) in Si‐rich particles like quartz. These results indicate that Si‐poor particles are an indicator that can be used to identify the Kosa‐derived particles grain by grain and to investigate transportation of the Kosa aerosol. This paper was by special invitation as a contribution to a special issue of the journal entitled “Application of Spectroscopic Methods to Environmental Problems”. The special issue was organized by Professor Peter A. Tanner, Professor in the Department of Biology and Chemistry at City University of Hong Kong.

Determining speciation of Pb in phosphate-amended soils: Method limitations

Determining the effectiveness of in situ immobilization for P-amended, Pb-contaminated soils has typically relied on non-spectroscopic methods. However in recent years, these methods have come under scrutiny due to technical and unforeseen error issues. In this study, we analyzed 18 soil samples via X-ray diffraction (XRD), selective sequential extraction (SSE), and a physiologically based extraction test (PBET). The data were compared against each other and to previous data collected for the soil samples employing X-ray absorption fine structure spectroscopy coupled with linear combination fitting (XAFS-LCF), which spectroscopically speciates and quantifies the major Pb species in the samples. It was observed that XRD was incapable of detecting pyromorphite, the hopeful endpoint of the immobilization strategy for reduced Pb bioavailability in our studies. Further, the SSE and PBET extraction methods demonstrated an increase of recalcitrant Pb forms in comparison to the XAFS-LCF results suggesting that SSE and PBET methods induced the precipitation of pyromorphite during the extraction procedures. The theme of this paper illustrates the experimental concerns of several commonly employed methods to investigate immobilization strategies of amended, metal-contaminated systems which may not be in true equilibrium. We conclude that appropriate application of spectroscopic methods provides more conclusive and accurate results in environmental systems (i.e., Pb, Zn, Cd, etc.) examining P-induced immobilization.

Cryptoporic and Isocryptoporic Acids from the Fungal Cultures of Polyporus arcularius and P. ciliatus.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Cryptoporic and isocryptoporic acids from the fungal cultures of Polyporus arcularius and P. ciliatus

In a chemical study of several fungal cultures of Polyporus, a methyl ester of cryptoporic H was isolated from P. ciliatus, together with cryptoporic acid H and 5-hydroxymethylfuran-3-carboxylic acid. Furthermore, two additional compounds, named isocryptoporic acids H and I, were isolated from P. arcularius. These isocryptoporic acids are isomers of the cryptoporic acids with drimenol instead of albicanol as the terpenoid fragment; their structural elucidation was determined by application of spectroscopic methods.