Utilizing FTIR-ATR spectroscopy for classification and relative spectral similarity evaluation of different Colletotrichum coccodes isolates

Colletotrichum coccodes (C. coccodes) is a pathogenic fungus which causes anthracnose on tomatoes and black dot disease in potatoes. It is important to differentiate among these isolates and to detect the origin of newly discovered isolates, in order to treat the disease in its early stages. However, distinguishing between isolates using common biological methods is time-consuming, and not always available. We used Fourier Transform Infra-Red (FTIR)-Attenuated Total Reflectance (ATR) spectroscopy and advanced mathematical and statistical methods to distinguish between different isolates of C. coccodes. To our knowledge, this is the first time that FTIR-ATR spectroscopy was used, combined with multivariate analysis, to classify such a large number of 15 isolates belonging to the same species. We obtained a success rate of approximately 90% which was achieved using the region 800-1775 cm(-1). In addition we succeeded in determining the relative spectral similarity between different fungal isolates by developing a new algorithm. This method could be an important potential diagnostic tool in agricultural research, since it may outline the extent of the biological similarity between fungal isolates. Based on the PCA calculations, we grouped the fifteen isolates included in this study into four different degrees of similarity.     

Direct identification and decongestion of Fermi resonances by control of pulse time ordering in two-dimensional IR spectroscopy

We show that it is possible to both directly measure and directly calculate Fermi resonance couplings in benzene. The measurement method used was a particular form of two-dimensional infrared spectroscopy (2D-IR) known as doubly vibrationally enhanced four wave mixing. By using different pulse orderings, vibrational cross peaks could be measured either purely at the frequencies of the base vibrational states or split by the coupling energy. This capability is a feature currently unique to this particular form of 2D-IR and can be helpful in the decongestion of complex spectra. Five cross peaks of the ring breathing mode nu13 with a range of combination bands were observed spanning a region of 1500-4550 cm(-1). The coupling energy was measured for two dominant states of the nu13+nu16 Fermi resonance tetrad. Dephasing rates were measured in the time domain for nu13 and the two (nu13+nu16) Fermi resonance states. The electronic and mechanical vibrational anharmonic coefficients were calculated to second and third orders, respectively, giving information on relative intensities of the cross peaks and enabling the Fermi resonance states of the combination band nu13+nu16 at 3050-3100 cm(-1) to be calculated. The excellent agreement between calculated and measured spectral intensities and line shapes suggests that assignment of spectral features from ab initio calculations is both viable and practicable for this form of spectroscopy.     

Temperature-dependent far-infrared spectra of single crystals of high explosives using terahertz time-domain spectroscopy

Survey spectra of single-crystal HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine), and PETN (pentaerythritol tetranitrate) were acquired in the region from 10 to 80 cm(-1) using terahertz time-domain spectroscopy. The spectra were taken at temperatures ranging from 8.4 to 300 K. Generally, the spectra show multiple absorption peaks in the range 50-80 cm(-1), with PETN (110) showing strong absorption features at room temperature. RDX (210) is the most notable in the region 10-40 cm(-1), showing multiple spectral features, while HMX (010) shows a very broad absorption at 47.8 cm(-1) with a fwhm of 37.3 cm(-1). Future plans include polarization-dependent investigations for multiple crystallographic orientations over an increased spectral range and higher-level theoretical calculations.     

Diffuse reflectance FTIR study of the interaction of alumina surfaces with ozone and water vapor

The interaction of ozone with alumina has been examined at ambient temperature as a function of ozone concentration and relative humidity. The experiments used diffuse reflectance FTIR spectroscopy in a small flow reactor, which provided control of the temperature, pressure, and composition of the gas mixture to which the sample was continuously exposed. Treatment of alumina with ozone produced a new spectroscopic feature at 1380 cm(-1), which we attribute to an aluminum oxide species formed by interaction of O3 with Lewis acid sites on the alumina surface. After exposure of the alumina sample to O3 was stopped, subsequent exposure of the sample to humidified nitrogen resulted in the slow removal of the peak at 1380 cm(-1). Simultaneously, the uptake of water by the alumina increased as indicated by the growth of the adsorbed water features which extend from approximately 3700 to 2500 cm(-1). Treatment of dry alumina with humidified ozone strongly inhibited both the rate of formation of the spectral feature at 1380 cm(-1) and its limiting extent of formation. These observations are analyzed in terms of the adsorption and surface reaction properties of ozone on alumina. The observation that the new oxide feature on alumina, produced by reaction with ozone, can be removed by water is important for assessing the ability of mineral dust aerosols to process atmospheric trace gases over a significant time scale. We believe the work reported here to be the first direct and quantitative kinetic study of the competition between O3 and water for adsorption sites on alumina.     

Infrared spectroscopy of large ammonia clusters as a function of size

We have measured the vibrational spectra of large ammonia (NH3)n clusters by photofragment spectroscopy in the spectral range from 3150 to 3450 cm(-1) for the average sizes n = 29, 80, 212, 447, and 989 and by depletion spectroscopy for n=8. The spectra are dominated by peaks around 3385 cm(-1) which are attributed to the asymmetric nu3 NH-stretch mode. Two further peaks between 3200 and 3260 cm(-1) have about equal intensity for n = 8 and 29, but only about 0.40 of the intensity of the nu3 peak for the larger sizes. The spectra for the smallest and largest size agree with those obtained by Fourier transform infrared spectroscopy in slit jet expansion and collision cells, respectively. By accompanying calculation we demonstrate that the energetic order of the spectral features originating from the bending overtone 2nu4 and the symmetric NH-stretch nu1 in the range from 3150 to 3450 cm(-1) is changed between n = 10 and 100, while the asymmetric NH-stretch nu3 only exhibits a moderate redshift. The reason is the coupling of the ground state modes to the overtones.     

Communication: Spectroscopic phase and lineshapes in high-resolution broadband sum frequency vibrational spectroscopy: resolving interfacial inhomogeneities of "identical" molecular groups

The ability to achieve sub-wavenumber resolution (0.6 cm(-1)) and a large signal-to-noise ratio in high-resolution broadband sum-frequency generation vibrational spectroscopy (HR-BB-SFG-VS) allows for the detailed SFG spectral lineshapes to be used in the unambiguous determination of fine spectral features. Changes in the structural spectroscopic phase in SFG-VS as a function of beam polarization and experimental geometry proved to be instrumental in the identification of an unexpected 2.78 ± 0.07 cm(-1) spectral splitting for the two methyl groups at the vapor/dimethyl sulfoxide (DMSO, (CH(3))(2)SO) liquid interface as well as in the determination of their orientational angles.     

Investigation of the low-frequency vibrations of crystalline tartaric acid using terahertz spectroscopy and solid-state density functional theory

The room temperature and cryogenic terahertz (THz) spectra (10-95 cm(-1)) of l-tartaric acid and dl-tartaric acid were investigated. At 293 K, the l-tartaric acid spectrum showed four absorption features at 36.4, 61.6, 78.7, and 87.3 cm(-1) in the experimental spectrum. Once cooled to 78 K, these features narrowed and shifted to 35.9, 63.4, 81.1, and 90.1 cm(-1). The THz spectrum of dl-tartaric acid is significantly different, containing only a single absorption at 79.9 cm(-1) at room temperature, which shifts to 82.9 cm(-1) at 78 K. Solid-state density functional theory calculations [B3LYP/6-311G(2d,2p)] were performed to simulate the crystalline structure of both molecular solids and to assign the observed spectral features to specific atomic motions. The THz spectrum of l-tartaric acid is particularly interesting in that it contains a theoretically unaccounted for spectral feature that may arise from second-order phonon processes and also exhibits an anomalous red-shifting absorption feature with cooling that is shown to originate from negative thermal expansion of the crystal.     

C-H stretching vibrations of methyl, methylene and methine groups at the vapor/alcohol (N = 1-8) interfaces

In IR and Raman spectral studies, the congestion of the vibrational modes in the C-H stretching region between 2800 and 3000 cm(-1) has complicated spectral assignment, conformational analysis, and structural and dynamics studies, even with quite a few of the simplest molecules. To resolve these issues, polarized spectra measurement on a well aligned sample is generally required. Because the liquid interface is generally ordered and molecularly thin, and sum frequency generation vibrational spectroscopy (SFG-VS) is an intrinsically coherent polarization spectroscopy, SFG-VS can be used for discerning details in vibrational spectra of the interfacial molecules. Here we show that, from systematic molecular symmetry and SFG-VS polarization analysis, a set of polarization selection rules could be developed for explicit assignment of the SFG vibrational spectra of the C-H stretching modes. These polarization selection rules helped assignment of the SFG-VS spectra of vapor/alcohol (n = 1-8) interfaces with unprecedented details. Previous approach on assignment of these spectra relied on IR and Raman spectral assignment, and they were not able to give such detailed assignment of the SFG vibrational spectra. Sometimes inappropriate assignment was made, and consequently misleading conclusions on interfacial structure, conformation and even dynamics were reached. With these polarization rules in addition to knowledge from IR and Raman studies, new structural information and understanding of the molecular interactions at these interfaces were obtained, and some new spectral features for the C-H stretching modes were also identified. Generally speaking, these new features can be applied to IR and Raman spectroscopic studies in the condensed phase. Therefore, the advancement on vibrational spectra assignment may find broad applications in the related fields using IR and Raman as vibrational spectroscopic tools.     

矿物元素指纹图谱的建立及在西洋参产地鉴别中的应用研究

采用电感稱合等离子体质谱法测定了山东、吉林、美国和加拿大4个产地西洋参中50种矿物元素的含量,研究了不同产地西洋参矿物元素的差别和转换系数,构建了西洋参的矿物元素指纹图谱.以各产地矿物元素含量的平均值构建了山东、吉林、美国和加拿大产西洋参的矿物元素标准指纹图谱.采用SPSS 20.0计算了各西洋参矿物元素指纹图谱与其矿...     

Spectral resolution in multivariate optical computing

An examination of spectral resolution effects on multivariate optical computing (MOC) and the design of multivariate optical elements (MOEs) is presented. A solution of napthalene and pyrene in CCl(4) is used as a test mixture, with spectra recorded in the nominal 2-2.5 microm spectral region at resolutions varying from 1 to 128 cm(-1). Spectra were treated in absorption mode and in transmission mode at sample pathlengths of 1, 0.5, and 0.2 cm. Principal components regression is used to provide comparison to MOE models. Conventional model prediction errors using all methods are presented as well as results of applying low-resolution models to high-resolution validation sets. This latter calculation is aimed at understanding the limits of calibration transfer when a model is based on spectra acquired with marginal spectral resolution. A theory is developed describing calibration transfer in the case of linear spectroscopy, which is shown to be consistent with the results observed in absorption mode and to represent the case of the short-pathlength limit in transmission mode. A definition of the necessary spectral resolution as a function of apodization function is given for linear spectroscopy, and a brief discussion of how non-linearity affects the results is provided.     

Application of two-dimensional near-infrared correlation spectroscopy to the discrimination of Chinese herbal medicine of different geographic regions

Fructus Lycii is a traditional Chinese medicinal herb. The objective of this paper was to apply two-dimensional (2D) near-infrared (NIR) correlation spectroscopy to the discrimination of Fructus Lycii of four different geographic regions. Generalized 2D-NIR correlation spectroscopy was able to enhance spectral resolution, simplify the spectrum with overlapped bands, and provide information about temperature-induced spectral intensity variations that was hard to obtain from one-dimensional NIR spectroscopy. The 2D synchronous and asynchronous spectra showed remarkable differences within the range of 4950-5700cm(-1) between samples of different geographic regions. Using NIR instead of IR made the 2D approach more convenient and fast, and it can be applied to more area like process control. This approach can also be applied analogously to the discrimination of other Chinese herbal medicine of different geographic regions.     

Raman spectroscopic and electrochemical characterization of myoglobin thin film: implication of the role of histidine 64 for fast heterogeneous electron transfer.

Myoglobin (Mb) thin films formed on various substrates have been characterized by using Raman spectroscopy, reflectance absorbance FT-IR, UV-vis absorption spectroscopy, and electrochemical methods. Raman spectra were obtained upon excitation within the Soret band as well as alpha-beta bands. The spin state marker bands observed from the Mb film in the 1550-1630 cm(-)(1) region (excitation at 514.5 nm) are approximately 20 cm(-)(1) higher than those of aqueous metMb having the high spin state. The 1210 cm(-)(1) band (methine bridge C-H vibration) also shifts to 1240 cm(-)(1) upon the formation of the film. These results indicate that the heme iron of myoglobin in the film is the ferric low-spin state, and the iron atom is pulled to the heme plane. A comparison of the Raman spectra of the Mb film with that of an Mb-imidazole derivative leads to the conclusion that the distal histidine is responsible for the change in the spectral characteristics. The escape of water from the sixth position upon the formation of the Mb film may result in a conformational change at the heme distal pocket: the histidine residue at the E7 helical position (H64) moves toward the central iron and is coordinated with it through the N on the imidazole ring. These structural features facilitate the fast electron transfer between the thin protein film and the electrode. Distal histidine may serve as an electron-transfer pathway as it does in cytochrome c.     

Hematite and carbonaceous materials in geological samples: a cautionary tale

Over the last few decades Raman spectroscopy has been increasingly applied as an analytical tool in geoscience research. Raman spectroscopy is a powerful tool for geologists as it is non-destructive, requires little to no sample preparation, and can be undertaken in situ on various irreplaceable geological samples. Also, this technique is useful in the identification of minerals and geo-organic material. However, despite this ease of application, there are some facets of Raman spectroscopy data that can lead to erroneous interpretations. For instance, there is much confusion in the geological literature distinguishing the difference between the hematite vibrational mode at ca. 1320 cm(-1) and the disordered sp(2) carbonaceous material D band at 1340 cm(-1). Furthermore, geologists will often collect 2 spectra, one in the mineral finger print region (200-800 cm(-1)) and then a spectrum in the carbon first-order region (1000-1800 cm(-1)), rather than performing a full-region scan. This allows the misidentification of the hematite mode at 1320 cm(-1) as the D band from disordered carbonaceous material. Here we show that it is best practice for geologists to collect spectra between 200 and 1800 cm(-1) to better distinguish between hematite and disordered carbonaceous material, materials that often co-occur in geological samples.     

Infrared spectral changes identified during different stages of herpes viruses infection in vitro

Microscopic Fourier transform infrared spectroscopy (FTIR) which is based on the characteristic molecular vibrational spectra of cells was previously applied for the identification of various biological samples. In the present study, FTIR spectroscopy was used for the characterization of different stages during the development of herpes viruses infection. Vero cells in culture were infected with high and low doses of different herpes viruses [herpes simplex virus types 1 and 2 (HSV-1, -2) or varicella-zoster virus (VZV)], and cellular changes were observed by optical and electron microscopy and analyzed by FTIR microscopy at different periods of time post-infection. Specific different spectral changes were observed at various stages of the viral infection development. The spectral intensity in the 1220-1260 cm(-1) region (mainly attributed to phosphate levels) was considerably increased in all infected cells compared to normal uninfected cells during the early stages of the viral infection development. However, at the late stages of the viral infection development (when all the cells in the infected culture lost their spindle shape and became circular) the spectral intensities in this region significantly decreased in the infected compared to the control cells. In addition, the peak at 1023 cm(-1), attributed to carbohydrates, almost fully disappeared at early stages of the viral infection development, whereas at late stages of the infection it raised to an equivalent or higher level than that of the uninfected control cells. These results support the potential of developing FTIR microspectroscopy as a simple, reagent free method for the early detection and accurate differentiation of different stages during the development of herpes virus infection.     

Near-infrared spectroscopy of autunites

NIR spectroscopy has been applied to the study water in the interlayer of the autunite minerals. The spectra of autunites and metaautunites in the first HOH fundamental overtone are different and the spectra of autunites of different origins in the 6000-7500 cm(-1) region are considerably different. A number of conclusions are made based upon the NIR spectra: (a) The spectra of different autunites are different in the NIR spectral region; (b) the spectra of metaautunites show similarity; (c) the spectra of metaautunites are different from that of autunites. NIR spectroscopy provides a method of determination of the structure of water in the interlayer of natural autunites. The implication from the variation in the NIR spectra is that the structural arrangement of water for different autunites is different and is sample dependent. NIR spectroscopy has a wide potential for the study of the autunite minerals.     

HCl adsorption and ionization on amorphous and crystalline H2O films below 50 K

Molecular beams were used to grow amorphous and crystalline H(2)O films and to dose HCl upon their surface. The adsorption state of HCl on the ice films was probed with infrared spectroscopy. A Zundel continuum is clearly observed for exposures up to the saturation HCl coverage on ice upon which features centered near 2530, 2120, 1760, and 1220 cm(-1) are superimposed. The band centered near 2530 cm(-1) is observed only when the HCl adlayer is in direct contact with amorphous solid water or crystalline ice films at temperatures as low as 20 K. The spectral signature of solid HCl (amorphous or crystalline) was identified only after saturation of the adsorption sites in the first layer or when HCl was deposited onto a rare gas spacer layer between the HCl and ice film. These observations strongly support conclusions from recent electron spectroscopy work that reported ionic dissociation of the first layer HCl adsorbed onto the ice surface is spontaneous.     

Spectroscopic characterization of omega-substituted biphenylthiolates on gold and their use as substrates for "on-top" siloxane SAM formation

Self-assembled monolayers (SAMs) of omega-substituted biphenylthiolates (omega-MBP) on gold were characterized by spectral ellipsometry, X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRRAS), and vibrational sum frequency generation spectroscopy (VSFG). The vibrational studies of the SAMs were supported by an ab initio frequency analysis at HF/6-31G and BP86/6-31G levels, yielding an assignment of all relevant spectral features in the range from 3500 to 1200 cm(-1). We were able to demonstrate that hydroxy-terminated MBP (HMBP) SAMs are basically featureless in the range of the CH stretching vibrations. Accordingly, the adsorption of a SAM of octadecyltrichlorosilane (OTS) on top of this model surface could be studied. A red shift of the C-O stretching vibration from 1281 to 1264 cm(-1) was observed during the chemisorption of OTS, thus allowing for a quantification of the number of OTS molecules involved in surface binding of OTS, which was found to be about 26% on average.     

近红外光谱测定人参与西洋参的主要皂甙总量

采用近红外光谱测定人参与西洋参的主要皂甙总量.采集人参与西洋参的漫反射光谱,分别对光谱进行正交信号校正(OSC)与常规预处理,建立了对应的偏最小二乘(PLS)回归模型.与常规最优预处理方法相比,OSC能很好地消除人参与西洋参的品种差异,显著提高了光谱与皂甙含量的相关系数,同时降低了PLS建模因子数,提高了模型的稳健性与...     

Two-dimensional laser induced fluorescence spectroscopy of van der Waals complexes: fluorobenzene-Ar(n) (n = 1,2)

The technique of two-dimensional laser induced fluorescence (2D-LIF) spectroscopy has been used to observe the van der Waals complexes fluorobenzene-Ar and fluorobenzene-Ar(2) in the region of their S(1)-S(0) electronic origins. The 2D-LIF spectral images reveal a number of features assigned to the van der Waals vibrations in S(0) and S(1). An advantage of 2D-LIF spectroscopy is that the LIF spectrum associated with a particular species may be extracted from an image. This is illustrated for fluorobenzene-Ar. The S(1) van der Waals modes observed in this spectrum are consistent with previous observations using mass resolved resonance enhanced multiphoton ionisation techniques. For S(0), the two bending modes previously observed using a Raman technique were observed along with three new levels. These agree exceptionally well with ab initio calculations. The Fermi resonance between the stretch and bend overtone has been analysed in both the S(0) and S(1) states, revealing that the coupling is stronger in S(0) than in S(1). For fluorobenzene-Ar(2) the 2D-LIF spectral image reveals the S(0) symmetric stretch van der Waals vibration to be 35.0 cm(-1), closely matching the value predicted based on the fluorobenzene-Ar van der Waals stretch frequency. Rotational band contour analysis has been performed on the fluorobenzene-Ar 0(0)(0) transition to yield a set of S(1) rotational constants A' = 0.05871 ± 0.00014 cm(-1), B' = 0.03803 ± 0.00010 cm(-1), and C' = 0.03103 ± 0.00003 cm(-1). The rotational constants imply that in the S(1) 0(0) level the Ar is on average 3.488 ? from the fluorobenzene centre of mass and displaced from it towards the centre of the ring at an angle of ~6° to the normal. The rotational contour for fluorobenzene-Ar(2) was predicted using rotational constants calculated on the basis of the fluorobenzene-Ar geometry and compared with the experimental contour. The comparison is poor which, while due in part to expected saturation effects, suggests the presence of another band lying beneath the contour.