Reactivity structural probes

Four forms of amine-reactive rhodamine probes are commonly available. Two of them are based on the tetramethyl derivatives of the fundamental rhodamine structure, one is based on the sulforhodamine B or Lissamine derivative, and the last is the sulforhodamine 101 or Texas Red-type of derivative. All of them react under alkaline conditions with primary amines in proteins and other molecules to form stable, highly fluorescent complexes. 

NHS-rhodamine is an amine-reactive fluorescent probe that contains a carboxy-succinimidyl ester group off the No. 5 or 6 carbons on rhodamine s lower-ring structure (Kellogg et al., 1988). The 5- and 6-isomers are virtually identical in their reactivity and fluorescent characteristics. Similar to TRITC (described previously), NHS-rhodamine can be used to label proteins and other macromolecules that contain primary amine groups. The isomeric forms of the fluorescent probe are available in mixed and purified forms (Invitrogen, Thermo Fisher). The pure forms are... 

Xu, G. Chance, M.R. Radiolytic modification and reactivity of amino acid residues serving as structural probes for protein footprinting. Anal. Chem. 2005, 77, 4549-4555. 

This chapter mainly focuses on the reactivity of 02 and its partially reduced forms. Over the past 5 years, oxygen isotope fractionation has been applied to a number of mechanistic problems. The experimental and computational methods developed to examine the relevant oxidation/reduction reactions are initially discussed. The use of oxygen equilibrium isotope effects as structural probes of transition metal 02 adducts will then be presented followed by a discussion of density function theory (DFT) calculations, which have been vital to their interpretation. Following this, studies of kinetic isotope effects upon defined outer-sphere and inner-sphere reactions will be described in the context of an electron transfer theory framework. The final sections will concentrate on implications for the reaction mechanisms of metalloenzymes that react with 02, 02 -, and H202 in order to illustrate the generality of the competitive isotope fractionation method. 

In addition to structural information, dynamic information can also be obtained through NMR. Time scales of both fast (picoseconds) and slow (seconds and longer) processes can be followed. Slow processes such as chemical reactivity are probed by following a change in an NMR property such as chemical shift or transfer of magnetization from one spectral site to another. Detailed kinetic information can be extracted in well-established experiments. Faster processes influence the NMR spin relaxation properties, such as Tt or T2, with kinetic information linked to the specific structure being examined. Model-independent ways... 

The research we describe in this paper addresses the fundamental nature of the active catalytic species in ionically supported systems. Structure and reactivity are probed using a variety of techniques, in order to make a detailed comparison of the supported and homogeneous catalysts. An important aspect of the study was to develop an in situ technique to follow the key organometallic reactions of the polymer-supported catalyst, and to obtain quantitative kinetic data for these reactions. 

As the reactivity is probed at a targeted microscopic region of the surface (often a single crystal face), it is possible to establish the relationship between surface structure and dissolution activity on the micrometer scale. 

Mu-substituted free radicals had not been detected by pSR at about 100 G which had been the magnetic field intensity commonly used in the muon facilities, and the first observation was made at high transverse magnetic fields (about 3000 G) in 1978 [11, 45] and this method has sometimes been called high-field pSR . A great number of radicals have been measured since then, e.g. olefins and dienes [46], methyl-, F- and other substituted benzenes [13, 47], and triple bonds [48]. All the observed radicals are derived by Mu addition to unsaturated molecules, and thus p is automatically located at the P-position, i.e. two bond, away from the unpaired electron or delocali system. Although Mu-substituted radicals are typical entities that are created by p" " and their structures and reactivities are probed by p itself, they are not ctealt with here in detail, since they have been fully reviewed [12,49]. 

G. Feher, M.Y. Okamura, and D. Kleinfeld, Electron transfer reactions in bacterial photosynthesis charge recombination kinetics as a structure probe, in "Protein Structure Molecular and Electronic Reactivity," R. Austin, E. Buhks, B. Chance, D. Devault, P.L. Dutton, H. Frauenfelder, and V.I. Goldanskii, eds.. Springer Ver-lag. New York (1987). 

Friedman J M 1994 Time-resolved resonance Raman spectroscopy as probe of structure, dynamics, and reactivity in hemoglobin Methods Enzymol. 232 205-31... 

Raman spectroscopy has provided information on catalytically active transition metal oxide species (e. g. V, Nb, Cr, Mo, W, and Re) present on the surface of different oxide supports (e.g. alumina, titania, zirconia, niobia, and silica). The structures of the surface metal oxide species were reflected in the terminal M=0 and bridging M-O-M vibrations. The location of the surface metal oxide species on the oxide supports was determined by monitoring the specific surface hydroxyls of the support that were being titrated. The surface coverage of the metal oxide species on the oxide supports could be quantitatively obtained, because at monolayer coverage all the reactive surface hydroxyls were titrated and additional metal oxide resulted in the formation of crystalline metal oxide particles. The nature of surface Lewis and Bronsted acid sites in supported metal oxide catalysts has been determined by adsorbing probe mole-... 

Let us now return to the question of solvolysis and how it relates to the stracture under stable-ion conditions. To relate the structural data to solvolysis conditions, the primary issues that must be considered are the extent of solvent participation in the transition state and the nature of solvation of the cationic intermediate. The extent of solvent participation has been probed by comparison of solvolysis characteristics in trifluoroacetic acid with the solvolysis in acetic acid. The exo endo reactivity ratio in trifluoroacetic acid is 1120 1, compared to 280 1 in acetic acid. Whereas the endo isomer shows solvent sensitivity typical of normal secondary tosylates, the exx> isomer reveals a reduced sensitivity. This indicates that the transition state for solvolysis of the exo isomer possesses a greater degree of charge dispersal, which would be consistent with a bridged structure. This fact, along with the rate enhancement of the exo isomer, indicates that the c participation commences prior to the transition state being attained, so that it can be concluded that bridging is a characteristic of the solvolysis intermediate, as well as of the stable-ion structure. ... 

Structure-reactivity relationships can be probed by measurements of rates and equiUbria, as was diseussed in Chapter 4. Direct comparison of reaction rates is used relatively less often in the study of radical reactions than for heterolytic reactions. Instead, competition methods have frequently been used. The basis of competition methods lies in the rate expression for a reaction, and the results can be just as valid a comparison of relative reactivity as directly measured rates, provided the two competing processes are of the same kinetic order. Suppose that it is desired to compare the reactivity of two related compounds, B—X and B—Y, in a hypothetical sequence ... 

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