Structure sensitivity secondary

C(C=0)C1 group to the precise structure (primary, secondary or tertiary) of the alkyl groups to which it is linked. However, our subsequent work with NO showed that its products are also sensitive to the alkyl structure yet in addition NO reacts with oxidized polymers to give distinctly different products from alcohol and hydroperoxide groups (see below). Consequently the COCl2 products were not explored further. 

Because protein ROA spectra contain bands characteristic of loops and turns in addition to bands characteristic of secondary structure, they should provide information on the overall three-dimensional solution structure. We are developing a pattern recognition program, based on principal component analysis (PCA), to identify protein folds from ROA spectral band patterns (Blanch etal., 2002b). The method is similar to one developed for the determination of the structure of proteins from VCD (Pancoska etal., 1991) and UVCD (Venyaminov and Yang, 1996) spectra, but is expected to provide enhanced discrimination between different structural types since protein ROA spectra contain many more structure-sensitive bands than do either VCD or UVCD. From the ROA spectral data, the PCA program calculates a set of subspectra that serve as basis functions, the algebraic combination of which with appropriate expansion coefficients can be used to reconstruct any member of the... 

Secondary a-tritium KIEs are much larger and more sensitive to a change in transition state structure than secondary a-deuterium KIEs. 

Abstract Now an incisive probe of biomolecular structure, Raman optical activity (ROA) measures a small difference in Raman scattering from chiral molecules in right- and left-circularly polarized light. As ROA spectra measure vibrational optical activity, they contain highly informative band structures sensitive to the secondary and tertiary structures of proteins, nucleic acids, viruses and carbohydrates as well as the absolute configurations of small molecules. In this review we present a survey of recent studies on biomolecular structure and dynamics using ROA and also a discussion of future applications of this powerful new technique in biomedical research. 

HPLC methods are well accepted for the rapid, selective, and highly efficient analytical scale separation and the semi-preparative recovery of proteins. CD spectral data measured in the UV have been instrumental in the interpretation of the secondary structure of the same macromolecules. Conceivably the coupling of these two techniques might provide extra specificity and structural sensitivity in the analysis of proteins [28,29]. 

Raman spectroscopy provides structure-sensitive bands for distinguishing these secondary structures. Assignments of the —CO—NH— group vibrations were first made via normal coordinate analysis on jV-methylacetamide by Miyazawa et al. (11). 

Ellipsometry and nonlinear optics have proven their sensitivity in studying monolayer thickness and molecular orientation, but generally the anisotropic nature of the interface makes results rather difficult to interpret [20-22], In many cases, these methods were limited in their potential to supply information about biophysical issues such as head group structure, enzyme secondary structure, and the orientation of ordered regions. 

The particle beam LC/FT-IR spectrometry interface can also be used for peptide and protein HPLC experiments to provide another degree of structural characterization that is not possible with other detection techniques. Infrared absorption is sensitive to both specific amino acid functionalities and secondary structure. (5, 6) Secondary structure information is contained in the amide I, II, and III absorption bands which arise from delocalized vibrations of the peptide backbone. (7) The amide I band is recognized as the most structurally sensitive of the amide bands. The amide I band in proteins is intrinsically broad as it is composed of multiple underlying absorption bands due to the presence of multiple secondary structure elements. Infrared analysis provides secondary structure details for proteins, while for peptides, residual secondary structure details and amino acid functionalities can be observed. The particle beam (PB) LC/FT-IR spectrometry interface is a low temperature and pressure solvent elimination apparatus which serves to restrict the conformational motions of a protein while in flight. (8,12) The desolvated protein is deposited on an infrared transparent substrate and analyzed with the use of an FT-IR microscope. The PB LC/FT-IR spectrometric technique is an off-line method in that the spectral analysis is conducted after chromatographic analysis. It has been demonstrated that desolvated proteins retain the conformation that they possessed prior to introduction into the PB interface. (8) The ability of the particle beam to determine the conformational state of chromatographically analyzed proteins has recently been demonstrated. (9, 10) As with the ESI interface, the low flow rates required with the use of narrow- or microbore HPLC columns are compatible with the PB interface. 

Primary structure sensitivity resulting from the effect of changing particle size on step and kink density appears therefore to be present here at short reaction times. Secondary structure sensitivity (including the effect of carbonaceous poisoning on the reaction rate) appears not to be present here. Thus Somorjai has reported that the dehydrogenation reaction of cyclohexane to cyclohexane is insensitive to both structural featureSt whereas the dehydrogenation of cyclohexene to benzene la very sensitive to the densities of atomic steps and kinks and the order of the carbonaceous overlayer on the platinum crystal surface. 

Manogue and Katzer (284) have proposed that structure sensitivity that arises from reaction-induced surface changes rather than from the intrinsic properties of the underlying metal be called secondary structure sensitivity. For the oxidation of NH3 over Pt/Al203 (285), it was observed that small particles deactivated faster than did large particles, enhancing the original antipathetic structure sensitivity of this system. 

To determine the degree to which chemical and morphological structures affect secondary bonding involving these sensitive amide and N-H groups, model compounds and polymers were used to study selected secondary bonding environments which mimic various degrees of phase separation and purity possible within the copolyether-ure-thane-urea. 

Ions are also used to initiate secondary ion mass spectrometry (SIMS) [ ], as described in section BI.25.3. In SIMS, the ions sputtered from the surface are measured with a mass spectrometer. SIMS provides an accurate measure of the surface composition with extremely good sensitivity. SIMS can be collected in the static mode in which the surface is only minimally disrupted, or in the dynamic mode in which material is removed so that the composition can be detemiined as a fiinction of depth below the surface. SIMS has also been used along with a shadow and blocking cone analysis as a probe of surface structure [70]. 

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