SI-ATRE

Figure 41 Si ATR spectrum for the residue on the polished metal plate (top) along with the three closest library matches. 

Finally, both samples were analyzed using ATR-FTIR spectroscopy. The Si ATR crystal was brought into contact with the sample, and spectra recorded. Figure 51 compares the spectra. Based on the excellent match factor between the spectra of the two samples (99.8%) and visual comparison of these two spectra,... 

ATR is one of the most useful and versatile sampling modes in IR spectroscopy. When radiation is internally reflected at the interface between a high-refractive index ATR crystal (usually Ge, ZnSe, Si, or diamond) and the sample, an evanescent wave penetrates inside the sample to a depth that depends on the wavelength, the refractive indices, and the incidence angle. Because the penetration depth is typically less than 2 pm, ATR provides surface specific information, which can be seen as an advantage or not if surface orientation differs from that of the bulk. It also allows one to study thick samples without preparation and can be used to characterize highly absorbing bands that are saturated in transmission measurements. 

Si element ATR-FTIR spectroscopy was used to analyze this residue, and its spectrum, along with the closest library matches, are shown in Figure 41. The absorbance of this residue is low as a consequence of the thin layer present on the plate. This makes matching the sample spectrum with a reference spectrum somewhat difficult. The closest matches extracted from the library interrogated are to ester-based plasticizer materials, which is consistent with a phthalate-plasticized PVC. A more specific identification could have been made with further testing such as subjecting the residue to GC-MS analysis, but the information suggested by the ATR-FTIR analysis was, in this case sufficient. 

Internal reflectance (attenuated total reflectance ATR ). The internal reflectance or, more usually, attenuated total reflectance (ATR), technique depends on the total reflectance of an IR beam at the internal face of an IR-transparent crystal of high IR refractive index, as shown in Figure 2.38. Medium 1 is a prism of such a material (for example, Si, Ge or KRS-5 [thallous bromide- iodide]), medium 2 is a thin coating of a metal (Au, Pt, Fe) which forms the working electrode and medium 3 is the electrolyte. The... 

Figure 2.39 (a) Schematic representation of the experimental arrangement for attenuated total reflection of infrared radiation in an electrochemical cell, (b) Schematic representation of the ATR cell design commonly employed in in situ 1R ATR experiments. SS = stainless steel cell body, usually coated with teflon P — Ge or Si prism WE = working electrode, evaporated or sputtered onto prism CE = platinum counter electrode RE = reference electrode T = teflon or viton O ring seals E = electrolyte. 

Figure 8.4 ATR-FTIR spectra of H—Si(lll) after exposure to air (a) in the dark, (b) with 450 nm (broadband) illumination, (c) with 350 nm (broadband) illumination, and (d) with Hg lamp illumination. Reprinted with permission from Reference [48], Copyright 2000 American Chemical Society.

The functionalization of H—Si(l 11) surfaces has been extended to the reaction with aldehydes. Indeed, H—Si(lll) reacts thermally (16 h at 85 °C) with decanal to form the corresponding Si—OCH2R monolayer that has been characterized by ATR-FTIR, XPS and atomic force microscopy (AFM) [63]. The reaction is thought to proceed either by a radical chain mechanism via adventitious radical initiation or by nucleophilic addition/hydride transfer. On the other hand, the reaction of H—Si(lll) with octadecanal activated by irradiation with a 150W mercury vapour lamp (21 h at 20-50 °C) afforded a R... 

Quayum, M. E., Kondo, T., Nihonyanagi, S., Miyamoto, D. and Uosaki, K. Formation of organic monolayer on a hydrogen terminated Si(l 11) surface via silicon-carbon bond monitored by ATR FT-IR and SFG spectroscopy Effect of orientational order on the reaction rate. Chemistry Letters, 208 (2002). 

Fig. 16. Change of the absorbance signal as a function of time for (a) cyclohexene and (b) TBHP on an uncoated ZnSe IRE (thin line) and on a ZnSe IRE coated with a methyl-modified Ti-Si aerogel catalyst (solid line). At time t = 0, the concentration at the inlet of the ATR flow-through cell was switched from 0 to 3 mmol/L, and at t = 122 s, it was switched back again (50).

Fig. 22. Demodulated ATR spectra representing adsorption/desorption of TBHP at room temperature on Ti-Si aerogels with various Ti contents and Si reference sample (OTi) lOTi (10% T1O2). 20Ti (20% TiO2). The TBHP concentration in cyclohexane was modulated between 0 and 3mmol/L (JO).

Fig. 25. ATR spectra recorded during epoxidation of cyclohexene catalyzed by a Ti-Si aerogel with TBHP as the oxidant under the influence of forced modulation of the cyclohexene concentration (a) time-resolved spectra (reference recorded before modulation) (b) difference spectra obtained by subtracting one (arbitrarily chosen) spectrum (c) phase-resolved (demodulated) spectra. The data set for the spectra in (a)-(c) is the same (SO).

Another label-free optical detection method—FTIR-ATR—has been applied for detection of thrombin by means of DNA aptamers [73], The antithrombin DNA aptamer previously developed by Tasset et al. [17] was immobilized covalently onto Si surface using UV irradiation method. As a quantitative measure, the area of N-H and CH2 bands was used. This method allowed to detect thrombin with a sensitivity around 10 nmol/L. The specificity of binding of protein to aptamer was also investigated using DNA with no binding site for thrombin. It has been noted that for effective binding study by FTIR-ATR method, the concentration of protein should be kept lower than 100 nmol/L. 

A typical set-up for a FTIR ATR experiment is described in Figure 1. A Brewster angle rotating Ge polarizer is place in the IR beam, in front of the C face of an ATR crystal, which can be made of Si, Ge, or ZnSe. A separate background spectra are recorded for the s- and p-polarization, and the crystal is used as a substrate either for LB or SA monolayer samples. 

As = 0 and Ap = dj. Vibrations that are perpendicular to the surface are more difficult to detect by ATR (usually we use grazing angle spectroscopy for this purpose). This is because of the fact that in the ATR mode djl < dellx. For example, the Ap values predicted for transitions perpendicular to the surface are smaller than those predicted for parallel transitions of same intrinsic intensity (transition moment dipoles) by factors of 2.22 (Ge), 2.10 (Si), and 1.67 (ZnSe). Therefore, it is recommended to use ZnSe when possible for analysis of molecules with both parallel and perpendicular transitions, and where grazing angle spectroscopy is not available. 

Tidwell CD, Ertel SI, Ratner BD, Tarasevich BJ, Atre S, Allara DL (1997) Langmuir 13 3404... 

Fig. 7. Baseline-corrected ATR-FTIR spectra through the NHS activation sequence discussed in the text (a) freshly prepared H/Si(lll), (b) after functionalization with undecylenic acid, (c) surface (b) reacted with NHS/EDC for 1 hour at room temperature and (d) surface (c) after reaction with TEGamine. The background used is the spectrum of a clean oxidized ATR Si(lll) crystal for (a) and the spectrum of a Si(lll)-H surface for (b) and (c). Reprinted from [53].

HREELS measurements have also facilitated observation of modes below 1500 cm 1 (including the important fingerprint region) not accessible in the ATR-FTIR experiments. Most notably, HREELS has been used to detect the Si-C stretch at 670 cm 1 on methyl [60] and hexyl [61] terminated surfaces, confirming the presence of a covalent link to the silicon surface. 

Fig. 9. HREELS spectra of functionalized silicon surfaces prepared via photochemical reactions with H/Si(lll). In each case R represents a saturated alkyl chain (9 or 10 carbon atoms long) covalently attached to the Si surface. The methyl and acid terminated surfaces were prepared via reactions with decene and undecylenic acid respectively while the thienyl terminated surface was prepared by reaction of thienyl Li with an ester terminated surface. The dashed line at 1500 cm-1 represents the typical low frequency cut-off for ATR-FTIR measurements on silicon.

The ATR-FTIR spectra of ENR and transmission spectra [158] of thin film of the coupling agent are shown in Figure 3.9b, in which the band at 1085 cm"1, is characteristic of Si—OCH3 stretching vibration, the band at 1602,1627 cm"1 are characteristic of NH2+ deformation modes and C=C (vinyl benzene) stretching, respectively. 

Fig. 8 p- and s-polarized in-situ-ATR-FTIR spectra of PLL/PMA-MS multilayers recorded after 10 deposition cycles on the untexturized (A) and on the uniaxially scratched Si substrate (B) in the presence of lm NaC104 (wet state) in the range 4000-1200 cm-1... 

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