Insights into molecular chemistry of Chiapas amber using infrared-light microscopy,PIXE/RBS,and sulfur K-edge XANES spectroscopy

Chiapas amber is a natural occurring fossil resin structurally composed of long macromolecule chains with semicrystalline phases associated with both fossil and polymerization process. The most conspicuous characteristic of this fossil polymer is that it preserves ancient organic inclusions. In the present work, PIXE/RBS spectrometry (particle-induced X-ray emission/Rutherford backscattering) were combined with complementary K-edge XANES spectroscopy (X-ray absorption near-edge structure) to identify the amount of sulfur in Chiapas amber. Initially, the amber samples were examined using infrared reflected photomicrography. Amber is transparent to infrared light and so embedded plants and animals are easily visible, showing them in extraordinary detail, as if they were immersed in a water-like solution. The PIXE/RBS data show that the proportion of sulfur in amber is significantly higher than that found in recently formed resins, consistent with the biogeochemical process that transforms the resin into amber during long-term burial in geological deposits. The sulfur K-edge XANES spectra from amber confirm the sulfur abundance and reveal sulfur species in the reduced and intermediate oxidation states in amber. Almost no oxidized sulfur was found, whereas the recent resins show mostly oxidized sulfur fractions. This indicates that labile oxidized sulfur decays during fossilization and resin maturation must occur under conditions of oxygen depletion. The implications of the presence of sulfur in amber for organic preservation is also discussed here. Sulfur compounds work as a polymer additive that promotes intense resin solidification. This restricts the early oxidant-specific biodegradation of the embedded biomatter and, over geological time, provides greater stability against chemical changes.     

Investigation of sulfur speciation in particles from small coal-burning boiler by XANES spectroscopy

Sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy was employed to study the speciation of sulfur in raw coal, ash by-product and fine particulate matter from a small coal-burning boiler. By means of least square analysis of the XANES spectra, the major organic and inorganic sulfur forms were quantitatively determined. The results show that about 70% of the sulfur in raw coal is present as organic and a minor fraction of the sulfur occurs as other forms: 17% of pyrite and 13% of sulfate. While in bottom ash, fly ash, and PM_2.5, the dominant form of sulfur is sulfate, with the percentage of 80,79 and 94, respectively. Moreover, a number of other reduced sulfur including thiophenic sulfur, element sulfur and pyrrhotite are also present. During coal combustion, most of organic sulfur and pyrite were oxidized and released into the atmosphere as SO₂ gas, part of them was converted to sulfate existing in coal combustion by-products, and a small part of pyrite was probably reduced to elemental sulfur and pyrrhotite. The results may provide information for assessing the pollution caused by small boiler and developing new methods for the control of SO₂ pollution.     

同步辐射软X射线近边吸收谱方法研究长期施肥对黑土有机氮官能团的影响

有机态氮是土壤氮素的主要存在形式,在农田生态系统氮循环中占有重要地位。了解土壤有机氮官能团组成,可为制定合理的农田管理措施提供科学依据。同步辐射软X射线近边吸收谱(N K-edge XANES)技术,是原位测定土壤有机氮官能团组成最有效的方法,但利用该技术对长期施肥条件下土壤有机氮官能团组成的研究尚未见报道。本试验利用N K-edge XANES方法,研究了长期(18年)不同施肥措施[即休闲(Fallow)、不施肥(CK)、施氮磷钾化肥(NPK)、有机肥配施化肥(NPKM)、1.5倍量的有机肥配施化肥(1.5NPKM)和玉米秸秆配施化肥(NPKS)]对黑土全土及粘粒中有机氮官能团的影响。结果表明：各处理均在401.2～401.6和402.7～403.1 eV范围内出现特征吸收峰,分别归属为酰胺/胺和吡咯类化合物,粘粒中特征吸收峰通常较全土更为明显。半定量分析结果指出,全土和粘粒均以酰胺/胺的相对比例最高,是有机氮官能团的主要存在形态;与休闲处理相比,对照处理中酰胺/胺的相对比例较低,而吡咯类氮的相对比例较高;有机无机配施条件下,酰胺/胺的相对比例随有机肥量的增加而下降,而吡咯类氮的相对比例则呈相反的变化趋势;全土中以NPKS处理的酰胺/胺相对比例最高,而粘粒中则以休闲处理的腈类/芳香氮相对比例最高。利用N K-edge XANES方法原位测定不同施肥措施下土壤有机氮官能团组成的变化是可行的。     

On the state of iron in a clinoptilolite

The characterization of an iron-containing natural zeolitic sample from the deposit of Tasajeras (Cuba) has been carried out by means of X-ray powder diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS),⁵⁷Fe Mössbauer spectroscopy and Fe K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). The results show that iron is mainly located (ca. 96%) as Fe³⁺ in an octahedral site of the clinoptilolite framework. No evidence of tetrahedrally coordinated Fe³⁺ was found. The remaining 4% Fe is located as Fe²⁺ in an extraframework octahedral site, probably as a solvated ion, within the clinoptilolite structure.     

Chemical states of nitrogen in ZnO studied by near-edge X-ray absorption fine structure and core-level photoemission spectroscopies

Interaction of low-energy nitrogen ions with ZnO surface has been studied by photoemission spectroscopy (PES) around N 1s core-level and near-edge X-ray absorption fine structure (NEXAFS) around N K-edge. Nitrogen can break Zn-O bonds at the surface and form N-O, Zn-N or Zn-N-O bonds, characterised by specific chemical shifts in PES or absorption peaks in NEXAFS. A distinctive signal from molecular nitrogen has also been observed in ion-bombarded samples in both NEXAFS and PES.     

In situ soft X-ray absorption spectroscopy of flames

The feasibility of in situ soft X-ray absorption spectroscopy for imaging carbonaceous species in hydrocarbon flames is demonstrated using synchrotron radiation. Soft X-rays are absorbed by core level electrons in all carbon atoms regardless of their molecular structure. Core electron spectroscopy affords distinct advantages over valence spectroscopy, which forms the basis of traditional laser diagnostic techniques for combustion. In core level spectroscopy, the transition linewidths are predominantly determined by the instrument response function and the decay time of the core–hole, which is on the order of a femtosecond. As a result, soft X-ray absorption measurements can be performed in flames with negligible Doppler and collisional broadening. Core level spectroscopy has the further advantage of measuring all carbonaceous species regardless of molecular structure in the far-edge region, whereas near-edge features are molecule specific. Interferences from non-carbon flame species are unstructured and can be subtracted. In the present study, absorption measurements in the carbon K-edge region are demonstrated in low-pressure (P _total = 20–30 Torr) methane jet flames. Two-dimensional imaging of the major carbonaceous species, CH₄, CO₂, and CO, is accomplished by tuning the synchrotron radiation to the respective carbon K-edge, near-edge X-ray absorption fine structure (NEXAFS) transitions and scanning the burner.     

NEXAFS characterization of DNA components and molecular-orientation of surface-bound DNA oligomers

Single stranded DNA oligomers (ssDNA) immobilized onto solid surfaces forms the basis for several biotechnological applications such as DNA microarrays, affinity separations, and biosensors. The surface structure of the surface-bound oligomers is expected to significantly influence their biological activity and interactions with the environment. In this study near-edge X-ray absorption fine structure spectroscopy (NEXAFS) is used to characterize the components of DNA (nucleobases, nucleotides and nucleosides) and the orientation information of surface-bound ssDNA. The K-edges of carbon, nitrogen and oxygen have spectra with features that are characteristic of the different chemical species present in the nucleobases of DNA. The effect of addition of the DNA sugar and phosphate components on the NEXAFS K-edge spectra was also investigated. The polarization-dependent nitrogen K-edge NEXAFS data show significant changes for different orientations of surface bound ssDNA. These results establish NEXAFS as a powerful technique for chemical and structural characterization of surface-bound DNA oligomers.     

A new technique to measure the differential XAFS spectrum

A new technique has been developed for direct measurement of the differential X-ray absorption fine structure(XAFS) spectrum by the energy-modulation method. To acquire the energy-oscillating incident X-ray beam, a piezoelectric actuator is used to control the double-crystal monochromator. A logarithmic converter circuit and a lock-in amplifier are used to extract the modulated signals. The normal and differential XAFS spectra of the Mn K-edge of Li2 Mn O3 have been collected. The X-ray-absorption near-edge-structure(XANES) spectra verify that the signal-to-noise ratio has been greatly improved by the new technique, and the extended X-ray absorption fine structure(EXAFS) spectra demonstrate that this new technique can efficiently enhance the signals of the backscattering atoms.     

Atomic structure of nickel phthalocyanine probed by X-ray absorption spectroscopy and density functional simulations

The local atomic structure of Ni in nickel phthalocyanine was studied by K-edge X-ray absorption fine structure spectroscopy. The obtained inter atomic nickel-nitrogen distance differs from the reference X-ray diffraction data so an additional study was performed within density functional theory framework. The justification of the used theoretical approach was provided by a comparison of theoretical free electron densities of states with experimental Ni K-edge X-ray absorption near edge spectra. The refined Ni local environment retain the reference structure of the molecule except for the length of Ni-N bond which increases to 1.90 Å.     

A comparative X-ray absorption near-edge structure study of bornite,Cu5FeS4, and chalcopyrite,CuFeS2

High resolution Fe L-, Cu L-, S L-edge and O K-edge X-ray absorption near-edge structure (XANES) spectra of synthetic bornite and the samples oxidized in air and leached in a ferric chloride solution have been recorded and compared with the spectra of chalcopyrite. The pre-edge shoulder in the Cu L-edge spectrum of bornite and the strong leading peak in the spectrum of chalcopyrite were attributed to the electron transitions to the minor density of unoccupied Cu 3d states, and the post-edge features were related to the states of s- and p-type. The Fe L-edge XANES showed the presence of predominant Fe²⁺ for chalcopyrite, and some quantity of Fe²⁺ for bornite cannot be excluded despite XPS and Mössbauer spectroscopy had previously detected only Cu⁺ and Fe³⁺ species in both minerals. The Cu L- and S L-edge spectra of bornite considerably modify and become similar to those of chalcopyrite after the oxidative leaching that produces the heavily metal-depleted surface layers, and the Fe L-edge XANES shows only a slightly increased contribution of Fe²⁺. The multiparticle configurations involving Fe²⁺ and Cu²⁺ or holes at S atoms may play a role in the L-spectra.     

Oxidation of the porous silicon surface under the action of a pulsed ionic beam: XPS and XANES studies

The changes in the electronic structure and phase composition of porous silicon under action of pulsed ionic beams have been studied by X-ray photoelectron spectroscopy (XPS) and X-ray absorption near-edge spectroscopy (XANES) using synchrotron radiation. The Si 2p and O 1s core photoemission spectra for different photoelectron collection angles, valence band photoemission spectra, and X-ray absorption near-edge fine structure spectrain the region of Si L _2,3 edges of the initial and irradiated samples have been analyzed. It has been found that, as a result of the irradiation, a thin oxide film consisting predominantly of higher oxide SiO₂ is formed on the porous silicon surface, which increases the energy gap of the silicon oxide. Such film exhibits passivation properties preventing the degradation of the composition and properties of porous silicon in contact with the environment.     

An x-ray absorption spectroscopic study of the electronic structure and bonding of rare-earth orthoferrites

Rare-earth orthoferrites, REFeO? (RE D rare earth; Y), are tremendously adaptable compounds that are being investigated for use in a wide variety of applications including gas sensors, vehicle catalytic converters, and solid-oxide fuel cells. They also exhibit interesting magnetic properties such as high-temperature antiferromagnetism, making them useful for data storage applications. The compounds adopt a distorted perovskite-type structure where the tilt angle of the octahedra increases (Fe-O-Fe bond angle decreases) as the size of the rare-earth atom decreases. Despite intensive study of the physical properties of these compounds, very few studies have investigated how the bonding and electronic structure of these systems change with substitution of the RE. X-ray absorption near-edge spectroscopy (XANES) is a technique well-suited for such a study, and, in view of this, Fe L-, Fe K- and O K-edge spectra from a series of REFeO? compounds (RE D La, Pr, Nd, Sm, Eu, Gd, Ho, Yb, Y) have been collected, and are presented here. Fe L-edge spectra show that Fe is octahedrally coordinated and that the Fe-centered octahedra do not appear to distort with changes in the identity of the RE. The Fe K-edge spectra contain an intersite hybrid peak, which is an ill-studied feature that is attributed to non-local transitions of 1s electrons to 3d states on the next-nearest-neighbor atom that are hybridized with 4p states on the absorbing atom through O 2p states. In this study, it is shown that the intensity of this feature is strongly dependent on the Fe-O-Fe bond angle; the lower the Fe-O-Fe bond angle, the less intense the intersite hybrid peak is.     

Structure comparison of Orpiment and Realgar by Raman spectroscopy

Raman spectroscopy was used to characterize and differentiate the two minerals, Orpiment and Realgar, and the bands related to the mineral structure. The Raman spectra of these two minerals are divided into three sections: (a) 100–250?cm^?1 region attributed to the sulfur–arsenic–sulfur bending vibrational modes; (b) 250–450?cm^?1 region due to the arsenic–sulfur stretching vibration; and (c) 450–850?cm^?1 region assigned to overtone and combination bands. A total of 14 Raman bands for the spectrum in the 1600–100?cm^?1 region were observed. The significant differences between the minerals Orpiment and Realgar are observed by Raman spectroscopy. Realgar shows the typical bands observed at 340, 268, 228, and 218?cm^?1, and the special bands at 379, 289, 200, 176, and 102?cm^?1 for Orpiment are observed. The additional bands in 850–450?cm^?1 region are only observed for the mineral Orpiment, which may be attributed to overtone and combination bands in the Raman spectrum. The variation in band positions is dependent upon the structural symmetry, arsenic–sulfur bond distances, and angles. Moreover, another cause for the difference is the effect of the intermolecular forces and to the strong coupling between close lying external and internal modes. The difference of these two minerals structure induce tremendous diversity on Raman spectra, so Raman spectroscopy offers the information on the molecular structure of the minerals Orpiment and Realgar.     

基于光谱分析的砷黄铁矿生物浸出过程中铁/砷/硫形态转化研究

基于同步辐射装置的As/S的K边及Fe的L边X射线吸收近边结构光谱(XANES)和X射线衍射(SR-XRD),结合扫描电镜(SEM)、傅里叶红外光谱(FTIR)、电感耦合等离子体发射光谱(ICP-AES)及各项浸出参数的测定,系统研究了(中度嗜热菌、嗜热硫化杆菌)浸出砷黄铁矿过程中铁、砷、硫的形态转化。结果表明,在生物作用下,砷黄铁矿的溶解速率明显高于化学浸出体系,伴随矿物溶解释放到溶液中的砷和铁在生物浸出体系中主要为As(Ⅴ)和Fe3+,而在无菌化学浸出体系则主要为As(Ⅲ)和Fe2+;细菌胞外多聚物(EPS)在细菌与硫化矿物的相互作用过程中起着至关重要的作用, FTIR的结果表明,生物浸出体系中吸附在矿物表面的吸附菌的EPS中蛋白质和多糖的含量均高于游离菌EPS;SEM的结果表明,砷黄铁矿表面在生物浸出过程中逐渐被腐蚀,且有浸出产物覆盖,而化学浸出10 d后,矿物表面依旧比较光滑;SR-XRD的结果表明,元素硫(S0)、黄钾铁矾和砷酸铁在生物浸出第4 d生成,并随时间延长逐渐累积,最终成为浸出渣中的主要成分。Fe的L边XANES结果表明,在细菌作用下矿物表面逐渐被Fe(Ⅲ)浸出产物覆盖;As的K边XANES结果表明,浸出渣中砷的价态包括As(-Ⅰ), As(Ⅲ)和As(Ⅴ),拟合结果表明,经过10 d的生物浸出,砷黄铁矿、雌黄(As2S3)和砷酸铁在矿渣中所占的比例分别为18.6%, 23.5%和57.9%,化学浸出10 d后,矿渣中除未溶解的砷黄铁矿外,仅有少量砷酸铁(6.2%)形成;S的K边XANES拟合结果表明,经过10 d的生物浸出,砷黄铁矿、 S0、硫代硫酸盐、施氏矿物和黄钾铁矾在矿渣中所占的比例分别为15.3%, 23.7%, 3.5%, 11.3%和46.2%,而在化学浸出10 d后的矿渣中,仅拟合到少量S0(7.8%)。基于上述结果可以得出,铁、砷、硫在砷黄铁矿生物作用下的形态转化过程分别为:Fe(Ⅱ)-Fe(Ⅲ), As(-Ⅰ)-As(Ⅲ)-As(Ⅴ), S-→S0→S2O■→SO■。结合溶液中的浸出参数发现,随着S0、黄钾铁矾、砷酸铁和雌黄的大量累积,砷黄铁矿的生物浸出严重受阻。硫代硫酸盐的生成表明砷黄铁矿的溶解途径与黄铁矿相似。     

Potassium doping effect on the lattice softening and electronic structure of Ba(1-x)K(x)Fe(2)As(2) probed by X-ray absorption spectroscopy

Ba(1-x)K(x)Fe(2)As(2) superconducting samples (x = 0, 0.2, 0.4, 0.5) were synthesized by the solid-state reaction method. In this contribution the doping effect of potassium on the lattice dynamics in this newly discovered Ba(1-x)K(x)Fe(2)As(2) superconductor has been investigated by extended X-ray absorption fine-structure spectroscopy. The analysis shows that with potassium doping an increased disorder in the iron layers is mainly related to the softening of the Fe-Fe bond. Information about the electronic structure of these materials has also been obtained by looking at the X-ray absorption near-edge structure spectra that point out the presence of holes in the Fe-3d/As-4p hybridized orbital of the BaFe(2)As(2)-based system.     

Adsorption and structure of methyl mercaptoacetate on Cu(1 1 1) surface by XPS and NEXAFS spectroscopy

Methyl mercaptoacetate (MA) on Cu(1 1 1) surface was investigated using synchrotron radiation-based X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. MA adsorbs on the surface via thiolate formation and weak interaction of the carbonyl group with the surface. Two different adsorption states previously reported for methanethiolate and ethanethiolate were confirmed, besides atomic sulfur. NEXAFS measurements support gauche-type conformation of MA whose skeleton lies on the surface.     

Calcium in ancient glazes and glasses: a XAFS study

Ceramic tiles used to manufacture artistic panels during the XVI to the XVIII centuries were decorated with high-lead soda-lime glazes, incorporating a diversity of chromophore cations, as ascertained by SRXRF (synchrotron radiation X-ray fluorescence). Previous X-ray absorption spectroscopy (XAS) studies have shown that sodium and lead are hosted by the glassy matrix in those glazes. However, the possible role of calcium as a modifier of the tetrahedral silica network is not fully clarified, despite being recognized that calcium cations alter some fundamental properties of glazes, namely transparency. An X-ray absorption fine structure (XAFS) study of glazes with varied colorings was therefore undertaken at Ca K- and L-edges. Well crystallized oxide minerals were used to model distinct coordination environments by oxygen atoms – close to octahedral geometry in calcite and dodecahedral in gypsum – while fluorite was chosen to mimic ideal cubic coordination. A first XAS approach suggested a minor variation in the energy separation between L₂–L₃ absorption edges when comparing blue and yellow glazes, irrespective of the period of manufacture. A further study on the X-ray absorption near-edge structure (XANES) carried out at the K-edge corroborated this difference and, along with the theoretical spectra modeling performed with the FEFF code, allowed interpreting of the Ca 1s absorption spectra of glazes as arising from a non-regular high-coordination environment within the silica matrix. PACS  61.43.Fs; 41.60.Ap; 61.10.Ht     

K‐edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration

Sulfur K‐edge XANES (X‐ray absorption near‐edge structure) spectroscopy is an excellent tool for determining the speciation of sulfur compounds in complex matrices. This paper presents a method to quantitatively determine the kinds of sulfur species in natural samples using internally calibrated reference spectra of model compounds. Owing to significant self‐absorption of formed fluorescence radiation in the sample itself the fluorescence signal displays a non‐linear correlation with the sulfur content over a wide concentration range. Self‐absorption is also a problem at low total absorption of the sample when the sulfur compounds are present as particles. The post‐edge intensity patterns of the sulfur K‐edge XANES spectra vary with the type of sulfur compound, with reducing sulfur compounds often having a higher post‐edge intensity than the oxidized forms. In dilute solutions (less than 0.3–0.5%) it is possible to use sulfur K‐edge XANES reference data for quantitative analysis of the contribution from different species. The results show that it is essential to use an internal calibration system when performing quantitative XANES analysis. Preparation of unknown samples must take both the total absorption and possible presence of self‐absorbing particles into consideration.     

X‐ray absorption spectroscopy at the Ni?K edge in Stackhousia tryonii Bailey hyperaccumulator

Young plants of Stackhousia tryonii Bailey were exposed to 34 mM Ni kg^?1 in the form of NiSO₄· 6H₂O solution and grown under controlled glasshouse conditions for a period of 20 days. Fresh leaf, stem and root samples were analysed in vivo by micro x‐ray absorption spectroscopy (XAS) at the Ni? K edge. Both x‐ray absorption near edge structure and extended x‐ray absorption fine structure spectra were analysed, and the resulting spectra were compared with spectra obtained from nine biologically important Ni‐containing model compounds. The results revealed that the majority of leaf, stem and root Ni in the hyperaccumulator was chelated by citrate. Our results also suggest that in leaves Ni is complexed by phosphate and histidine, and in stems and roots, phytate and histidine. The XAS results provide an important physiological insight into transport, detoxification and storage of Ni in S. tryonii plants. Copyright © 2008 John Wiley & Sons, Ltd.