Attenuated Total Reflection Spectra Research Articles

Understanding Advanced Attenuated Total Reflection Correction: The Low Absorbance Assumption.

We present an attenuated total reflection (ATR) correction scheme capable of rectifying ATR spectra while considering the polarization state for arbitrary angles of incidence, provided that this angle exceeds the critical angle for the entire ATR spectrum. Due to its reliance on the weak absorption approximation, it cannot achieve perfect correction of the ATR spectra. However, comprehending its functionality may offer valuable insights into the concept behind the weak absorption approximation. Depending on the specific polarization state of an instrument accessory combination, this correction scheme may outperform the proprietary advanced ATR correction authored by ThermoFisher while being as user-friendly, but in contrast to the latter completely transparent with regard to its functionality.

Multimodal fiber probe for simultaneous mid-infrared and Raman spectroscopy

A fiber probe has been developed that enables simultaneous acquisition of mid-infrared (MIR) and Raman spectra in the region of 3100–2600 cm−1. Multimodal measurement is based on a proposed ZrO2 crystal design at the tip of an attenuated total reflection (ATR) probe. Mid-infrared ATR spectra are obtained through a pair of chalcogenide infrared (CIR) fibers mounted at the base of the crystal. The probe enables both excitation and acquisition of a weak Raman signal from a portion of the sample in front of the crystal using an additional pair of silica fibers located in a plane perpendicular to the CIR fibers. The advantages of combining MIR and Raman spectra in a single probe have been discussed.

Saccharomyces cerevisiae CellWall Remodeling in the Absence of Knr4 and Kre6 Revealed by Nano-FourierTransform Infrared Spectroscopy.

The cell wall integrity (CWI) signaling pathway regulates yeast cell wall biosynthesis, cell division, and responses to external stress. The cell wall, comprised of a dense network of chitin, β-1,3- and β-1,6- glucans, and mannoproteins, is very thin, <100 nm. Alterations in cell wall composition may activate the CWI pathway. Saccharomyces cerevisiae, a model yeast, was used to study the role of individual wall components in altering the structure and biophysical properties of the yeast cell wall. Near-field Fourier transform infrared spectroscopy (nano-FT-IR) was used for the first direct, spectrochemical identification of cell wall composition in a background (wild-type) strain and two deletion mutants from the yeast knock-out collection: kre6Δ and knr4Δ. Killer toxin resistant 6 (Kre6) is an integral membrane protein required for biosynthesis of β-1,6-glucan, while Knr4 is a cell signaling protein involved in the control of cell wall biosynthesis, in particular, biosynthesis and deposition of chitin. Complementary spectral data were obtained with far-field (FF)-FT-IR, in transmission, and with attenuated total reflectance (ATR) spectromicroscopy with 3-10 μm wavelength-dependent spatial resolution. The FF-FT-IR spectra of cells and spectra of isolated cell wall components showed that components of the cell body dominated transmission spectra and were still evident in ATR spectra. In contrast, the nano-FT-IR at ∼25 nm spatial resolution could be used to characterize the yeast wall chemical structure. Our results show that the β-1,6-glucan content is decreased in kre6Δ, while all glucan content is decreased in the knr4Δ cell wall. The latter may be thinner than in wild type, since not only are mannan and chitin detectable by nano-FT-IR, but also lipid membranes and protein, indicative of cell interior.

Sophisticated Attenuated Total Reflection Correction Within Seconds for Unpolarized Incident Light at 45°.

The most common mid-infrared (MIR) attenuated total reflection (ATR) accessory has a nominal angle of incidence of 45° and does not have a polarizer. A spectrum recorded with such an accessory does not hold enough information for the sophisticated ATR correction of MIR spectra with strong peaks, which are often strongly affected by refractive index changes due to anomalous dispersion. Here we show that a 45° ATR spectrum recorded without a polarizer and the polarization angle for the same ATR Fourier transform infrared spectroscopy system provide enough information to determine the ATR s-polarized spectrum. Further analysis with an improved non-iterative Kramers-Kronig analysis immediately yields the complex refractive index function. The analysis is about two orders of magnitude faster than iterative formalism and runs within seconds on a typical office PC. The effectiveness of our advanced ATR correction formalism is showcased through its application to water, employing diamond, ZnSe, and Ge ATR crystals, along with two distinct ATR accessories. Additionally, the formalism is applied to octadecane spectra. Potential sources of errors such as incidence angle spread, dispersion of the polarization angle, and the influence of reflection at the air/ATR crystal interface are investigated by simulations.

Rapid and portable mid-infrared analysis of wet sediment samples by a novel “filter-press” attenuated total reflectance method

Mid-infrared (MIR) analysis of wet sediments or soils usually requires freezing and drying, adding considerable analysis time and cost, and promoting changes in chemical properties. A novel attenuated total reflectance (ATR) mid-infrared (MIR) method was developed to enable analysis of non-processed, aqueous sediments. Wet sediment samples from the Coorong Lagoon, South Australia, were subjected to laboratory analysis for physical and chemical properties, our new filter-press ATR method, and conventional ATR and diffuse reflectance (DRIFT) analysis of dried samples. For ATR on wet sediments, samples were pressed onto the ATR crystal with a filter-paper backing and scanned. The spectra were analyzed by principal components analysis (PCA) and partial least squares regression (PLSR) to develop multivariate models for total organic carbon (TOC). ATR spectra of as-received wet sediments were poor due to water absorption features, but filter-pressing reduced these and greatly enhanced the solids spectral component. The filter-pressed PLSR cross-validation for TOC resulted in an R2 = 0.89 and RMSECV = 0.78%. Prediction accuracies were similar to freeze-dried ATR samples and far more accurate than testing wet samples without filter-pressing. Our findings confirmed the filter-press ATR method as proof-of-concept and showed that it has the potential to remove one of the major barriers to in-field application of MIR techniques, the high and variable amounts of moisture levels commonly present in many environmental samples. Extension of the filter-press ATR method to a wider range of analytes may enable it to rapidly acquire moist or wet sediment and soil property data while in the field.

Application of Optical Photothermal Infrared (O-PTIR) Spectroscopy for Assessment of Bone Composition at the Submicron Scale.

The molecular basis of bone structure and strength is mineralized collagen fibrils at the submicron scale (∼500 nm). Recent advances in optical photothermal infrared (O-PTIR) spectroscopy allow the investigation of bone composition with unprecedented submicron spatial resolution, which may provide new insights into factors contributing to underlying bone function. Here, we investigated (i) whether O-PTIR-derived spectral parameters correlated to standard attenuated total reflection (ATR) Fourier transform infrared spectroscopy spectral data and (ii) whether O-PTIR-derived spectral parameters, including heterogeneity of tissue, contribute to the prediction of proximal femoral bone stiffness. Analysis of serially demineralized bone powders showed a significant correlation (r = 0.96) between mineral content quantified using ATR and O-PTIR spectroscopy, indicating the validity of this technique in assessing bone mineralization. Using femoral neck sections, the principal component analysis showed that differences between O-PTIR and ATR spectra were primarily attributable to the phosphate ion (PO4) absorbance band, which was typically shifter toward higher wavenumbers in O-PTIR spectra. Additionally, significant correlations were found between hydrogen phosphate (HPO4) content (r = 0.75) and carbonate (CO3) content (r = 0.66) quantified using ATR and O-PTIR spectroscopy, strengthening the validity of this method to assess bone mineral composition. O-PTIR imaging of individual trabeculae at 500 nm pixel resolution illustrated differences in submicron composition in the femoral neck from bones with different stiffness. O-PTIR analysis showed a significant negative correlation (r = -0.71) between bone stiffness and mineral maturity, reflective of newly formed bone being an important contributor to bone function. Finally, partial least squares regression analysis showed that combining multiple O-PTIR parameters (HPO4 content and heterogeneity, collagen integrity, and CO3 content) could significantly predict proximal femoral stiffness (R2 = 0.74, error = 9.7%) more accurately than using ATR parameters. Additionally, we describe new findings in the effects of bone tissue orientation in the O-PTIR spectra. Overall, this study highlights a new application of O-PTIR spectroscopy that may provide new insights into molecular-level factors underlying bone mechanical competence.

Effects of fine grinding on mid-infrared spectroscopic analysis of plant leaf nutrient content

Fourier transform mid infrared (FT-MIR) spectroscopy combined with modeling techniques has been studied as a useful tool for multivariate chemical analysis in agricultural research. A drawback of this method is the sample preparation requirement, in which samples must be dried and fine ground for accurate model calibrations. For research involving large sample sets, this may dramatically increase the time and cost of analysis. This study investigates the effect of fine grinding on model performance using leaf tissue from a variety of crop species. Dried leaf samples (N = 300) from various environmental conditions were obtained with data on 11 nutrients measured using chemical methods. The samples were scanned with attenuated total reflectance (ATR) and diffuse reflectance (DRIFT) FT-MIR techniques. Scanning was repeated after fine grinding for 2, 5, and 10 min. The spectra were analyzed for the 11 nutrients using partial least squares regression with a 75%/25% split for calibration and validation and repeated for 50 iterations. All analytes except for boron, iron, and zinc were well-modeled (average R2 > 0.7), with higher R2 values on ATR spectra. The 5 min level of fine grinding was found to be most optimal considering overall model performance and sample preparation time.

Use of polarized ATR measurements to simplify referencing in continuous sample monitoring by absorption spectroscopy

Using the difference in the effective path lengths of perpendicular- and parallel-polarized light in attenuated total reflectance (ATR) spectroscopy, we demonstrated acquisition of infrared (IR) absorption spectra without needing periodic measurements of a standard reference such as an empty optical cell. With a liquid sample constantly in contact with the ATR internal reflection element (IRE), we used the perpendicular-polarized signal, which has lower effective path length, as the reference signal, and the parallel-polarized signal, as the sample signal. To demonstrate the validity of this method and the need for periodic measurements of a standard reference in the conventional method, we measured unpolarized and polarized ATR spectra of air and isooctane using a Fourier transform infrared (FTIR) spectrometer on two consecutive days. For the conventional method, we used the unpolarized signals of air and isooctane to calculate the absorbance and showed that there were some artifacts with baseline curvature when the air signal from day 1 was used with the isooctane signal from day 2, but not when we used the air and isooctane signals from the same day. The artifacts were due to some inevitable drifts in the instrument between days; hence, the air signal must be measured as often as the instrument drift demands. With the proposed method, we showed that the absorption spectra could be approximately reproduced between days without any measurements of air. The proposed method merits consideration for process analytical technology (PAT) applications for example of continuous flow through an ATR cell where the introduction of a new substance (e.g., air or vacuum) for periodic baseline measurements is non-trivial.

Traditions, anomalies, mistakes and recommendations in infrared spectrum measurement for wood

This paper deals with the difficulties of infrared spectroscopy measurement and suggests ways of dealing with them. Many problems appear when applying ATR (attenuated total reflection) measurement for determining the absorbance spectrum of wood, especially the highly porous nature of wood which does not fulfil the requirements of ATR measurement. Correct ATR spectrum determination requires wavelength dependence correction, but some authors miss out doing this. Normalisation of the infrared (IR) spectrum is a useful data manipulation method for correct evaluation of the spectra, but the incorrect normalisation can destroy the spectrum preventing the evaluation of the spectrum appropriately. Examples are given to teach the correct normalisation process. The difference spectrum method is an excellent tool to present the changes in IR spectra, but only a few scientists use it. Usage of wavenumbers during IR spectrum presentation is a traditional method nowadays. However, the usage of wavelength gives a more expressive spectrum presentation than wavenumber if the whole wavelength interval is presented in one diagram.

SPECTRA OF ATTENUATED TOTAL REFLECTION OF NITRIDED SiO2/Si STRUCTURES

We studied the behavior of nitrogen in silicon dioxide films on single-crystal silicon substrates by the attenuated total reflection (ATR) method and time-of-flight secondary ion mass spectrometry. Nitrogen was introduced into a dielectric formed by pyrogenic oxidation at a temperature of 850 ºС in an atmosphere of wet oxygen by implantation of N+ ions with an energy of 40 keV at doses of 2.5‧1014 and 1.0‧1015 cm–2,&#x0D; followed by rapid thermal annealing at a temperature of 1000 or 1050 ºС with a duration of 15 s in air. Nitridization of some of the samples was carried out during thermal annealing in a nitrogen atmosphere with the addition of a small amount of oxygen at a temperature of 1200 ºС for 120 minutes. It is established that during heat treatments, the majority of nitrogen atoms diffuse to the SiО2/Si interface and accumulate in the near-boundary region of the oxide. The ATR spectra show an absorption band with maxima at ~2320 and 2360 cm–1, which is probably due to vibrations of double cumulative bonds of the O=Si=N− type. The formation of these bonds is due to the interaction of nitrogen with dangling bonds at the silicon-dielectric interface, as a result of which uncompensated or strained bonds are replaced by more stable ones. The resulting stronger chemical bonds prevent charge accumulation on the surface of the SiО2/Si interface.

SOMSpec as a General Purpose Validated Self-Organising Map Tool for Rapid Protein Secondary Structure Prediction From Infrared Absorbance Data.

A protein’s structure is the key to its function. As protein structure can vary with environment, it is important to be able to determine it over a wide range of concentrations, temperatures, formulation vehicles, and states. Robust reproducible validated methods are required for applications including batch-batch comparisons of biopharmaceutical products. Circular dichroism is widely used for this purpose, but an alternative is required for concentrations above 10 mg/mL or for solutions with chiral buffer components that absorb far UV light. Infrared (IR) protein absorbance spectra of the Amide I region (1,600–1700 cm−1) contain information about secondary structure and require higher concentrations than circular dichroism often with complementary spectral windows. In this paper, we consider a number of approaches to extract structural information from a protein infrared spectrum and determine their reliability for regulatory and research purpose. In particular, we compare direct and second derivative band-fitting with a self-organising map (SOM) approach applied to a number of different reference sets. The self-organising map (SOM) approach proved significantly more accurate than the band-fitting approaches for solution spectra. As there is no validated benchmark method available for infrared structure fitting, SOMSpec was implemented in a leave-one-out validation (LOOV) approach for solid-state transmission and thin-film attenuated total reflectance (ATR) reference sets. We then tested SOMSpec and the thin-film ATR reference set against 68 solution spectra and found the average prediction error for helix (α + 310) and β-sheet was less than 6% for proteins with less than 40% helix. This is quantitatively better than other available approaches. The visual output format of SOMSpec aids identification of poor predictions. We also demonstrated how to convert aqueous ATR spectra to and from transmission spectra for structure fitting. Fourier self-deconvolution did not improve the average structure predictions.

Ispitivanje strukturnih delova zrna hibrida kukuruza ZP 677 metodom IC ometene totalne refleksije

In this paper, the grain and structural parts of the grain of maize hybrid ZP 677 were studied, using Infrared Spectroscopy - Attenuated Total Reflectance (ATR). The ATR spectra of grain, endosperm, pericarp and germ of maize hybrid are characterized by a number of bands, band intensity, band kinetics and band location distribution in the wavelength range 400 cm-1 to 4000 cm-1. These parameters were specifically tested for both, the grain and the endosperm, pericarp and germ. Spectral bands that are very high and high intensity usually range from 3 to 5, characterized by different intensity, kinetic forms, as well as by the distribution of origin in the wavelength range. These spectral bands enable the identification of the following organic compounds: proteins, carotenoids, ethers, cellulose, lipids, carboxylic acids, amino acids, protein amides, alkanes, sugars, carbohydrates, ketones, alcohols, phenols, aldehydes and amines. Spectral bands of grains, endosperm, pericarp and germs that are low and very low intensity are also characterized by the number of bands, low bandwidth, distribution of the place of origin, and especially by the oscillation frequency of valence bonds of functional groups of organic molecules. Spectral bands that are low and very low intensity enable the identification of organic molecules, compounds and their fragments, as well as the identification of various forms of excited states of molecular structures and excited states of valence bonds of organic molecules. The excited state of molecular structures and the excited state of valence bonds of functional groups of organic molecules are manifested in various forms of oscillatory motion. Examples of functional groups of organic molecules in which all the mentioned excited states of molecular structures and excited states of valence bonds occur are alcohols, amines, alkynes, ketones, alkenes, ester, lipids, carbonyl group (ester), amides, nitrogen-hydrogen group, (NH), primary amines, carboxylic acids, amides, acid chlorides, nitrites, amides, carbonyl group (amide), aliphatic carbon-hydrogen bond and aldehydes.

Diamond-Coated Silicon ATR Elements for Process Analytics

Infrared attenuated total reflection (ATR) spectroscopy is a common laboratory technique for the analysis of highly absorbing liquids or solid samples. However, ATR spectroscopy is rarely found in industrial processes, where inline measurement, continuous operation, and minimal maintenance are important issues. Most materials for mid-infrared (MIR) spectroscopy and specifically for ATR elements do not have either high enough infrared transmission or sufficient mechanical and chemical stability to be exposed to process fluids, abrasive components, and aggressive cleaning agents. Sapphire is the usual choice for infrared wavelengths below 5 µm, and beyond that, only diamond is an established material. The use of diamond coatings on other ATR materials such as silicon will increase the stability of the sensor and will enable the use of larger ATR elements with increased sensitivity at lower cost for wavelengths above 5 µm. Theoretical and experimental investigations of the dependence of ATR absorbances on the incidence angle and thickness of nanocrystalline diamond (NCD) coatings on silicon were performed. By optimizing the coating thickness, a substantial amplification of the ATR absorbance can be achieved compared to an uncoated silicon element. Using a compact FTIR instrument, ATR spectra of water, acetonitrile, and propylene carbonate were measured with planar ATR elements made of coated and uncoated silicon. Compared to sapphire, the long wavelength extreme of the spectral range is extended to approximately 8 μm. With effectively nine ATR reflections, the sensitivity is expected to exceed the performance of typical diamond tip probes.

Dyakonov surface magnons and magnon polaritons

We predicted one Dyakonov surface magnon (DSM) and two Dyakonov magnon polaritons (DSMPs) localized at the antiferromagnet (AF)-air interface. Their concise dispersion equations and necessary conditions of existence were obtained. The DSM is the magnetostatic limit of the first DSMP, which are situated inside the AF reststrahlen frequency band. The second DSMP has no magnetostatic limit and lies outside the frequency band. The specifical frequency ranges occupied by the DSM and DSMPs were analytically found. The DSMPs are hybrid-polarization surface polaritons and the DSM is a hybrid-polarization surface magnetostatic mode. The first DSMP possesses large attenuation constants so that it is highly localized at the surface. Compared with it, the second DSMP exhibits relatively small attenuation constants. According to the features of polarization obtained for either DSMP, we used the TE and TM radiations incident on the AF surface to calculate attenuated total reflection (ATR) spectra, respectively. These ATR spectra not only further prove the existence of the DSMPs but also demonstrate their observability in experiment. However, the DSM should be detected by means of a light-scattering technique.

Radiation-Induced Processes in Diazoquinone–Novolac Resist Films under Irradiation with 60Co γ-Rays

The processes occurring under the irradiation of FP9120 diazoquinone–novolac resist films on silicon with 60Co γ-rays have been studied by attenuated total reflectance (ATR) FTIR spectroscopy. It has been found that a significant modification of the ATR spectra of the photoresist films was noticeable only at absorbed doses above 200 kGy, and it occurred due to the radiation-induced transformations of methyl, methylene, hydroxymethyl, and phenoxyl groups of phenol–formaldehyde resin and o-naphthoquinone diazide (a photosensitive component). At the same time, the ATR spectra exhibited no signs of the destruction of aromatic fragments in the resist at doses to 300 kGy. In the region of the stretching vibrations of C=O bonds, a decrease in the maximum intensity of a band at ~1700 cm–1 was observed upon irradiation with its simultaneous broadening and shift to the high-energy region by ~30 cm–1 due to a change in the nearest environment of the C=O group. An increase in the absorption band intensity at 1650 cm–1 indicated the accumulation of formaldehyde upon the γ-irradiation of the resist as a result of the fragmentation of hydroxymethyl residues in the phenol–formaldehyde resin.

Optical Theory-Based Simulation of Attenuated Total Reflection Infrared Spectra of Montmorillonite Films

AbstractInfrared analyses of clay mineral samples are usually performed by transmission techniques. While transmission measurements are easy and inexpensive, the sample preparation plays a critical role in the quality of the data. Alternatively, attenuated total reflection (ATR) provides a powerful and often simpler analysis method. However, the ATR spectra reveal significant differences when compared to transmission spectra sometimes leading to confusion in the interpretations. Indeed, optical effects play a prominent role in the ATR spectral profile and their identification is mandatory for obtaining quantitative information regarding molecular/particle orientation or film thickness. The objective of the present study was to perform exact spectral simulations of montmorillonite films by making use of optical theory, including the determination of the anisotropic optical constants from the experimental reflectance spectra by Kramers-Kronig (KK) transformation. This methodology was used: (1) to choose the appropriate optical conditions for advanced and reliable characterization of clay minerals; (2) to extract quantitative information such as the estimation of the film thickness; and (3) to discriminate optical phenomena (optical interferences) from chemical/structural features of the sample.

High Sensitive Biosensors Based on the Coupling Between Surface Plasmon Polaritons on Titanium Nitride and a Planar Waveguide Mode.

High sensitivity biosensors based on the coupling of surface plasmon polaritons on titanium nitride (TiN) and a planar waveguide mode were built; they were proved by sensing three different media: air, water and dried egg white; sensors described here could be useful for sensing materials with a refractive index between 1.0 and 1.6; in particular, materials of biological interest with a refractive index in the range 1.3–1.6, like those containing biotin and/or streptavidin. They were built by depositing Nb2O5/SiO2/TiN multilayer structures on the flat surface of D-shaped sapphire prisms by using the dc magnetron sputtering technique. Attenuated total reflection (ATR) experiments in the Kretschmann configuration were accomplished for the air/TiN/Prism and S/Nb2O5/SiO2/TiN/Prism structures, S being the sample or sensing medium. ATR spectra for plasmons at the TiN/air interface showed a broad absorption band for angles of incidence between 36 and 85°, with full width at half maximum (FWHM) of approximately 40°. For the S/Nb2O5/SiO2/TiN/Prism structures, ATR spectra showed a sharp reflectivity peak, within the broad plasmonic absorption band, which was associated with Fano resonances. The angular position and FWHM of the Fano resonances strongly depend on the refractive index of the sensing medium. ATR spectra were fitted by using the transfer-matrix method. Additionally, we found that angular sensitivity and figure of merit increase with increasing the refractive index of the sensing medium.

Bidentate cation-anion coordination in the ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate supported by vibrational spectra and NBO, AIM and SQMFF calculations

Experimental attenuated total reflectance (ATR) and Raman spectra for the synthesized ionic liquid 1-Ethyl-3-methylimidazolium hexafluorophosphate [EMIM+][PF6−] have been combined with the functional hybrid B3LYP and the 6-31G∗ and 6-311++G∗∗ basis sets in order to evaluate the coordination mode of [PF6−] anion and determine the its structural, electronic, topological and vibrational properties. The scaled quantum mechanical force fields (SQMFF) methodology allowed us to obtain a set of scaled force constants fitting the observed wavenumbers because, so far, they have not reported. Experimental ATR and Raman spectra for the ionic liquid [EMIM+][PF6−] in the solid phase are consistent with the corresponding predicted by using both levels of theory. Here, complete vibrational assignments of 72 normal modes of vibration expected for ionic liquid were performed by using B3LYP/6-311++G∗∗ level and considering that the [PF6−] anion adopts a bidentate coordination mode. Atomic Merz-Kollman (MK) charges and bond orders studies have revealed a distorted octahedral symmetry of anion in the ionic liquid and have suggested bidentate coordination of anion by two C–H⋯F hydrogen bonds, as experimentally was also proposed. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations support the high stability of ionic liquid and its high dipole moment value. Frontier orbitals for the three species show that the [PF6−] anion increases the reactivity of ionic liquid. Here, we determine that the B3LYP/6-311++G∗∗ molecular force field for the ionic liquid [EMIM+][PF6−] with the bidentate coordination mode adopted by [PF6−] anion is well represented, as also was supported by the scaled force constants calculated for both C–H⋯F hydrogen bonds.

Evaluation of surface roughness of metal films using plasmonic Fano resonance in attenuated total reflection

Attenuated total reflection (ATR) by surface plasmon polariton (SPP) is a method for evaluating the dispersion relation of SPP from the position of a dip in the reflection spectrum. However, recent studies have shown that the dips are displaced from SPP resonance because they are produced by a type of Fano resonance, i.e., the interference between the resonant reflection process accompanied by resonant excitation of SPP and the direct reflection process without resonant excitation. This result suggests that the system properties difficult to be achieved in the dispersion relation of SPP can be characterized using the ATR method. In this study, we investigate the effect of surface roughness due to nanosized dimples created in the initial stage of pitting corrosion on the ATR spectrum, from the viewpoint of Fano resonance. Using the temporal coupled-mode method, it is shown that the Fano resonance in ATR is caused by the phase change of direct reflection because of the absorption on the metal surface, and the spectral shape is determined by this phase, along with the ratio of the external (radiative) decay rate to the total decay rate of the resonant mode. Moreover, it is clarified that the internal and external decay rates extracted from the ATR spectrum provide information on corrosion, such as the effective thickness of the metal film and the randomness in dimple distribution.

Transformation of aqueous protein attenuated total reflectance infra-red absorbance spectroscopy to transmission.

Infrared (IR) spectroscopy is increasingly being used to probe the secondary structure of proteins, especially for high-concentration samples and biopharmaceuticals in complex formulation vehicles. However, the small path lengths required for aqueous protein transmission experiments, due to high water absorbance in the amide I region of the spectrum, means that the path length is not accurately known, so only the shape of the band is ever considered. This throws away a dimension of information. Attenuated total reflectance (ATR) IR spectroscopy is much easier to implement than transmission IR spectroscopy and, for a given instrument and sample, gives reproducible spectra. However, the ATR-absorbance spectrum varies with sample concentration and instrument configuration, and its wavenumber dependence differs significantly from that observed in transmission spectroscopy. In this paper, we determine, for the first time, how to transform water and aqueous protein ATR spectra into the corresponding transmission spectra with appropriate spectral shapes and intensities. The approach is illustrated by application to water, concanavalin A, haemoglobin and lysozyme. The transformation is only as good as the available water refractive index data. A hybrid of literature data provides the best results. The transformation also allows the angle of incidence of an ATR crystal to be determined. This opens the way to using both spectral shape and spectra intensity for protein structure fitting.