Investigation of the structures and absorption spectra for some hemicyanine dyes with pyridine nucleus by TD-DFT/PCM approach

Density-functional theory calculations of the Rayleigh optical activities of small isolated polyglycine molecules are reported. Fully extended β-sheet-like conformations of polypeptides of glycine, (Gly)_n (with n=1–5) are considered. After geometry optimizations, dipole moments and dipole polarizabilities (both the mean and the anisotropic components) are calculated using the B3LYP and B3P86 functionals in three basis sets. The polarizabilities are used to analyze the Rayleigh scattering activities and depolarization ratios. The convergence of the average dipole polarizability per monomer is analyzed. The differences in activity and depolarization for Rayleigh scattered radiation between the extended β-sheet-like and the folded -helix-like forms of tetraglycine are analyzed and found to be relevant, suggesting its possible use in experimental characterization.     

Infrared spectra of geminal and novel triple hydroxyl groups on silica surface

We investigated the O---H stretching frequencies of geminal and triple hydroxyl groups on silica surface by FT-IR spectroscopy. The geminal and triple hydroxyl groups were individually prepared by the chemical reaction of alkylchlorosilane with surface isolated hydroxyl groups which are separated enough and following hydroxylation of surface chlorine groups. The O---H stretching frequencies of these generated geminal and triple hydroxyl groups were observed at frequencies by 2 and 3 cm⁻¹ lower than that of isolated ones, respectively. By heat treatment the triple hydroxyl groups are firstly eliminated, and secondly the geminal hydroxyl groups disappear. Lastly only isolated hydroxyl groups remain on silica surface.     

Effects of carbon dioxide captured from ambient air on the infrared spectra of supported amines

Amino groups in highly dense coatings of amines on solid supports react with CO₂ of ambient air and form ammonium-carbamate ion pairs. These ion pairs change the properties of the amine-modified supports. In numerous studies, the corresponding infrared (IR) spectra have been misinterpreted. The presumption has been that such ion pairs would not form in ambient air, and therefore IR bands have been assigned to moieties of the support and the amines. Here, we discuss common misunderstandings of the IR spectra of amine-modified supports and highlight that proper sample handling is necessary before employing different characterization techniques. We exemplify by performing an IR spectroscopic study of a propylamine-modified porous silica. Such amine-modified supports are relevant to applications in gas separation, catalysis, controlled drug delivery and adsorption of pollutants from water.     

Calibration model transfer for near-infrared spectra based on canonical correlation analysis

In order to solve the calibration transformation problem in near-infrared (NIR) spectroscopy, a method based on canonical correlation analysis (CCA) for calibration model transfer is developed in this work. Two real NIR data sets were tested. A comparative study between the proposed method and piecewise direct standardization (PDS) was conducted. It is shown that the transfer results obtained with the proposed method based on CCA were better than those obtained by PDS when the subset had sufficient samples.     

Comparative study of various normal mode analysis techniques based on partial Hessians

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine‐stretch, the spectrum of quinine and a bis‐cinchona derivative, and the low frequency modes of the LAO binding protein. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

The effect of cryogenic sample cooling on X-ray absorption spectra

It is common for samples to be cooled to near liquid He temperature (4 K) during measurement of their X-ray absorption spectra (XAS). This procedure is believed to improve spectrum quality either by minimizing radiation damage, or by decreasing thermal motions of atoms. The actual benefits realized by cooling are rarely assessed, since that would require duplicate measurements at multiple temperatures, followed by duplicate data analyses. With a cryostat installed, it is difficult to measure room temperature or hotter spectra, which often requires removing the cryostat from the beam path.Here we investigate the effect of cooling and show that it is not globally useful in X-ray absorption spectroscopy. Photolysis does not occur, or its consequences are not controlled by cooling. Secondary photochemical damage is delayed and is remote from the absorption site. Thermal motions do not usually contribute significantly to disorder and consequent damping of EXAFS, either because vibrational amplitudes are small, or because static disorder and structural complexity affect EXAFS in the same way but more profoundly.The low probability of photochemical effects on XAS is in contrast to the situation with crystallography of biological specimens, where photochemical damage anywhere in the sample degrades the data set regardless of proximity to atoms of one specific element. Thermal disorder becomes important in certain types of samples and when the Debye-Waller factor is itself used as a tool. In most cases, it is more efficient to first measure room temperature spectra, and then repeat measurement using a cryostat of only those spectra where the objectives of the analysis justify an attempt to gain more information.     

Adsorption of pyridine on a polycrystalline gold electrode surface studied by infrared reflection absorption spectroscopy

The adsorption behavior of pyridine on a smooth polycrystalline gold electrode surface was investigated over a wide wavenumber region (2000–500 cm⁻¹) by in situ infrared reflection absorption spectroscopy (IRAS). The reversible adsorption/desorption of pyridine was observed upon the change in applied electrode potential, and the adsorption state at positive potentials was found to depend strongly on the kind of halide ion used as a supporting electrolyte. Symmetry analysis of absorption bands observed revealed that pyridine molecules adsorb with the molecular axis (C₂ axis) perpendicular to the electrode surface (vertical configuration) at positive potentials in 0.5 M KF, KCl and KBr solutions. A band due to the out-of-plane bending mode of the adsorbed pyridine molecule was observed at potentials more negative than ca. 0 V for 0.5 M KF solution containing 100 mM pyridine. We concluded that even in the 100 mM pyridine solution, adsorbed pyridine forms a monolayer and that the molecules reorient from a flat (parallel) to the vertical configuration as the potential becomes less negative. No bands due to adsorbed pyridine were detected for 0.5 M KI solution. The amount of adsorbed pyridine was found to depend strongly on the strength of specific adsorption of halide ions.     

基于染料吸收光谱的光导纤维pH传感器

基于固定化染料吸收光谱的原理,本文研究了将染料指示剂固定于阴离子交换膜上而制成的光导纤维pH传感器.实验结果与理论相符.固定化作用引起了染料pKa值的变化,也引起了吸收波长的位移,所提出的六个传感器可用于pH1.6-11.0范围内不同区间的pH测量.对传感器的响应特性及其影响因素也进行了必要的探讨.     

Effect of peripheral substitution on the electronic absorption and fluorescence spectra of metal-free and zinc phthalocyanines

The effect of substituents on the position and intensity of the electronic absorption and fluorescence spectra of phthalocyanines (Pcs) was examined for 35 Pc compounds. When electron-releasing groups are bound to four alpha-benzo positions of the Pc skeleton, the B and Q bands shift to longer wavelength. Relative to this shift, the effect of introducing the same electron-releasing groups at the other four alpha positions amounts to about 1.6-2.0. Although the effect is not always clearly seen, introduction of electron-releasing groups in the beta-benzo positions of the Pc skeleton generally shifts the Q band to shorter wavelength. The effect of electron-withdrawing groups is exactly the opposite with respect to the alpha and beta positions. These effects can be reasonably explained by considering the magnitude of the atomic orbital coefficients of the carbon atoms derived from molecular orbital (MO) calculations. In addition, the following intriguing phenomena were observed in the experiments, although not all were explained theoretically: 1) the splitting of the Q band of metal-free Pcs decreases with increasing wavelength of the Q band, 2) the ring currents of Pcs with Q bands at longer wavelength are generally smaller, and 3) the absorption coefficients of the Q band of Pc compounds with 16-electron-releasing substituents are larger than those of the corresponding tetra- and octasubstituted Pcs by several tens of percent. 4) Our PPP calculations suggested that the absorption coefficient of the Q band of Pcs with more strongly electron releasing substituents is larger. 5) The second HOMO of the Pcs with the Q band at longer wavelength has b(1u) symmetry, as opposed to the a(2u) symmetry of normal Pcs. 6) Pcs showing S1 emission maxima at wavelengths longer than about 740 nm generally have quantum yields of less than 0.1.     

Interpretation of IR spectra of epoxysaccharides based on the theoretical calculation of frequencies and intensities of normal vibrations

A detailed assignment of absorption bands in IR spectra of methyl 3,4-anhydro-α-D-talo-hexapyranoside and methyl 2,3-anhydro-4-deoxy-α-D-ribo-hexapyranoside is first made based on the complete calculation of frequencies and absolute intensities of normal vibrations of molecules and their comparison with the corresponding experimental values. The effect of the epoxy group on the bands characteristic of the pyranose ring is analyzed. The charactericity of spectral features of oxymethyl substitution for the hydroxyl group and the oxirane ring is studied.     

基于分子参数的药物小肠吸收预测模型

选择100个化合物作为数据集,随机选取其中80个为训练集,其他分子为验证集,并为每个化合物分子计算了30个参数.通过采用五种不同多元线性回归分析方法对其训练模拟,建立了数学模型,并用验证集检验了所建模型的预测能力.结果发现向后筛选法为最优小肠吸收建模方法.由该法所建模型的统计结果良好(R2>0.80),应用于验证集时也表现出较强预测能力.该模型确定了对小肠吸收影响较大的分子参数,有助于指导进一步的新药筛选和开发.     

Vibrational spectra and normal coordinate analysis of two isotopomers of the thiosulfate ion

The Raman spectra of ¹⁸O-thiosulfate ion (S₁O⁻²₃) in H₁¹⁸O solution and the IR spectrum of ¹⁸O-sodium thiosulfate in the solid have been obtained. Normal Coordinate calculations fitting all the fundamental wavenumbers of both ¹⁶O and ¹⁸O isotopomers have been carried out transferring the GVFF of the sulfate ion as the starting point and employing a symmetry force field for the least-squares adjustment procedure. A comparison of the results is made with the known force fields for several sulfur compounds.     

Quantitative analysis of multiple components based on liquid chromatography with mass spectrometry in full scan mode

Although liquid chromatography with mass spectrometry in full scan mode can obtain all the signals simultaneously in a large range and low cost, it is rarely used in quantitative analysis due to several problems such as chromatographic drifts and peak overlap. In this paper, we propose a Tchebichef moment method for the simultaneous quantitative analysis of three active compounds in Qingrejiedu oral liquid based on three‐dimensional spectra in full scan mode of liquid chromatography with mass spectrometry. After the Tchebichef moments were calculated directly from the spectra, the quantitative linear models for three active compounds were established by stepwise regression. All the correlation coefficients were more than 0.9978. The limits of detection and limits of quantitation were less than 0.11 and 0.49 μg/mL, respectively. The intra‐ and interday precisions were less than 6.54 and 9.47%, while the recovery ranged from 102.56 to 112.15%. Owing to the advantages of multi‐resolution and inherent invariance properties, Tchebichef moments could provide favorable results even in the situation of peaks shifting and overlapping, unknown interferences and noise signals, so it could be applied to the analysis of three‐dimensional spectra in full scan mode of liquid chromatography with mass spectrometry.     

多模型共识偏最小二乘法用于近红外光谱定量分析

将多模型共识偏最小二乘法用于近红外光谱定量分析。利用随机抽取的训练子集建立一系列偏最小二乘模型,选取其中性能较好的部分模型作为成员模型,用这些成员模型来预测未知样品。将该方法用于一组生物样本的近红外光谱与样品中人血清白蛋白、γ-球蛋白以及葡萄糖含量之间的建模研究,并与单模型偏最小二乘法了进行比较。结果 PLS对独立测试集中三种组分进行50次重复预测的平均RMSEP分别为0.1066,0.0853和0.1338,RMSEP的标准偏差分别为0.0174,0.0144和0.0416;而本方法重复预测的平均RMSEP分别为0.0715,0.0750和0.0781,RMSEP的标准偏差分别为0.0033,0.2729×10-4和0.0025。     

Preparation and characterization by surface-enhanced infrared absorption spectroscopy of silver nanoparticles formed on germanium substrates by electroless displacement

In this paper, the feasibility of applying electroless displacement to prepare silver nanoparticles (AgNPs) on the surface of germanium (Ge) substrate is demonstrated, and the performances of surfaces prepared in this manner for surface-enhanced infrared absorption (SEIRA) spectroscopy are reported. The process used to produce suitable AgNPs for SEIRA by electroless deposition is simple and effective, requiring only pretreatment of the germanium surface with hot air, immersion of the substrate in a dilute solution of silver nitrate, and washing of the resulting plate. To quantify the behavior of AgNPs on a Ge substrate and to optimize the conditions for the preparation of AgNPs on Ge substrates, a monolayer of p-nitrothiophenol (PNTP) was bonded to the surface of the AgNPs by immersion of the plate in a dilute solution of PNTP and measurement of the transmission spectrum. The factors that influenced the formation of AgNPs, and hence the SEIRA signals, included the concentration of AgNO₃, the reaction time and the temperature. Results indicated that stronger absorption bands in the SEIRA spectrum of a monolayer of PNTP were obtained if the reaction rate for the displacement of silver ions by Ge was slow. This condition was achieved by keeping the concentration of AgNO₃ and the reaction temperature low. Under the optimal conditions found in this work, an enhancement factor of approximately 100 was achieved for commonly used probe molecules in SEIRA measurements.     

Infrared, and Raman spectra, conformational stability, normal coordinate analysis, ab initio calculations, and vibrational assignment of 1-chlorosilacyclobutane

The infrared spectra (3500–40 cm⁻¹) of gaseous and solid and the Raman spectra (3500–30 cm⁻¹) of liquid and solid 1-chlorosilacyclobutane, c-C₃H₆SiClH, have been obtained. Both the axial and equatorial conformers with respect to the chlorine atom have been identified in the fluid phases. Variable temperature (−105 to −150°C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 211±17 cm⁻¹ (2.53±0.21 kJ/mol), with the equatorial conformer being the more stable form and the only conformer remaining in the annealed solid. At ambient temperatures, approximately 26% of the axial conformers are present in the vapor phase. A complete vibrational assignment is proposed for the equatorial conformer, and many of the fundamentals of the axial conformers have also been identified. The vibrational assignments are supported by normal coordinate calculations utilizing ab initio force constants. Complete equilibrium geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities, and depolarization ratios have been determined for both rotamers by ab initio calculations employing the 6-31G(d) basis set at the levels of restricted Hartree–Fock (RHF) and/or Moller–Plesset (MP) to second order. Structural parameters have also been obtained using MP2/6-311+G(d,p) ab initio calculations. The r₀ parameters for both conformers are obtained from a combination of the ab initio predicted values and the twelve previously reported microwave rotational constants. The results are discussed and compared to those obtained for some similar molecules.     

Rapid analysis of flavonoids based on spectral library development in positive ionization mode using LC-HR-ESI-MS/MS

Natural product screening in plants has always been a difficult task due to the complex nature of the plant material and diverse structures of the compounds present in them. Flavonoids are important and diverse class of plant secondary metabolites with numerous medicinal activities. The present study focuses on the development of a high-resolution tandem mass spectral library for the rapid and authentic identification of common flavonoids. A total of forty flavonoid standards belong to class flavones, isoflavones, flavanones, flavanols and anthocyanins were pooled into two solutions applying logP-based strategy. The flavonoids were analyzed using LC-QTOF-MS high-resolution mass spectrometer with optimization of different instrumental parameters to achieve good sensitivity. The library was built by incorporating names, molecular formulae, exact masses, and MS, and MS/MS spectra of analyzed flavonoids using Bruker Library Editor tool. The fragmentation pattern observed for the standard compounds were compared to the fragments reported in the literature. To assess the practical implications, an extract of tea sample was analyzed and screened using the developed library, which resulted in the identification of three common flavonoids based on their HR-ESI-MS/MS spectral features. The established LC-HR-MS/MS method can be used for the targeted identification of flavonoids in complex samples like food material from different botanical families.     

Discrimination of transgenic tomatoes based on visible/near-infrared spectra

VIS-NIR spectroscopy combined with multivariate analysis after the appropriate spectral data pre-treatment has been proved to be a very powerful tool for judgment of the relative pattern of the objects that have very similar properties. In this study, seventy transgenic tomatoes with antisense LeETR2 and 94 of their parents, non-transgenic ones were measured in VIS-NIR diffuse reflectance mode. Principal component analysis (PCA), discriminant analysis (DA) and partial least-squares discriminant analysis (PLSDA) were applied to classify tomatoes with different genes into two groups. Calibrations were developed using PLS regression with the leave-one-out cross-validation technique. The results show that differences between transgenic and non-transgenic tomatoes do exist and excellent classification can be obtained after optimizing spectral pre-treatment. The correct classifications for transgenic and non-transgenic tomatoes were both 100% using PLSDA after derivative spectral pre-treatment. The raw spectra with PLSDA model after the second derivative pre-treatment had the best satisfactory calibration and prediction abilities, with r_c = 0.97964, root mean square error of calibration (RMSEC) = 0.099, r_cv = 0.97963, root mean square error of cross-validation (RMSECV) = 0.0993 and a factor. The results in the present study show VIS-NIR spectroscopy together with chemometrics techniques could be used to differentiate transgenic tomato, which offers the benefit of avoiding time-consuming, costly and laborious chemical and sensory analysis.     

Study on difference between epidermis, phloem and xylem of Radix Ginseng with near-infrared and infrared spectroscopy coupled with principal component analysis

Ginseng is a precious traditional Chinese herbal medicine. Different parts of ginseng are deemed to have different medicinal values and properties. Rapid and non-destructive methods, such as diffuse reflectance near-infrared spectroscopy (DR-NIR), Fourier transform infrared spectroscopy with attenuated total reflectance (ATR-FTIR), were used to evaluate the differences of epidermis, phloem and xylem in ginseng, respectively. Samples were grounded into 200-mesh fine powder or cut into slices with about 2 mm thickness for DR-NIR and ATR-FTIR spectra measurement, respectively. To explore the classifications between different parts of ginseng, the spectra of DR-NIR and ATR-FTIR were pretreated to calculate first derivative and then was analyzed with principal component analysis (PCA). The PCA results of DR-NIR spectra indicate that epidermis and xylem part of ginseng have distinct difference, and even different positions of epidermis or xylem part show regular and gradual differences. ATR-FTIR spectra directly show that three parts of ginseng are different at 2920, 2852, 1736 and 925.7 cm⁻¹ peaks, especially for epidermis of ginseng. The PCA results of ATR-FTIR spectra yield clear classifications of the three parts of ginseng.     

Comprehensive data analysis of femtosecond transient absorption spectra: A review

Nowadays, time-resolved spectroscopy data can be routinely and accurately collected in UV-vis femtosecond transient absorption spectroscopy. However, the data analysis strategy and the postulation of a physically valid model for this kind of measurements may be tackled with many different approaches ranging from pure soft-modeling (model-free) to hard-modeling, where the elaboration of a parametric spectro-temporal model may be required. This paper reviews methods that are used in practice for the analysis of femtosecond transient absorption spectroscopy data. Model-based methods, common in photochemistry, are revisited, and soft-modeling methods, which originate from the chemometrics field and that recently disseminated in the photo(bio)chemistry literature, are presented. These soft-modeling methods are designed to suit the intrinsic nature of the multivariate (or multi-way) measurement. Soft-modeling tools do not require a priori physical or mechanistic models to provide a decomposition of the data on the time and wavelength dimensions, the only requirement being that these two (or more) dimensions are separable. Additionally, Bayesian data analysis, which provides a probabilistic framework for data analysis, is considered in detail, since it allows uncertainty quantification and validation of the model selection step.