Probes, molecular

These procedures proposed by Dubinin and by Stoeckli arc, as yet, in the pioneer stage. Before they can be regarded as established as a means of evaluating pore size distribution, a wide-ranging study is needed, involving model micropore systems contained in a variety of chemical substances. The relationship between the structural constant B and the actual dimensions of the micropores, together with their distribution, would have to be demonstrated. The micropore volume would need to be evaluated independently from the known structure of the solid, or by the nonane pre-adsorption method, or with the aid of a range of molecular probes. 

If a Type I isotherm exhibits a nearly constant adsorption at high relative pressure, the micropore volume is given by the amount adsorbed (converted to a liquid volume) in the plateau region, since the mesopore volume and the external surface are both relatively small. In the more usual case where the Type I isotherm has a finite slope at high relative pressures, both the external area and the micropore volume can be evaluated by the a,-method provided that a standard isotherm on a suitable non-porous reference solid is available. Alternatively, the nonane pre-adsorption method may be used in appropriate cases to separate the processes of micropore filling and surface coverage. At present, however, there is no reliable procedure for the computation of micropore size distribution from a single isotherm but if the size extends down to micropores of molecular dimensions, adsorptive molecules of selected size can be employed as molecular probes. 

Studies on covalent hydration of N-heterocycles (67AG(E)919,76AHC(20)117) have revealed the diagnostic value of alkyl substituents in structural assignments due to their steric hindrance effects in addition reactions. C-Methyl substituents are therefore also considered as molecular probes to solve fine-structural problems in the pteridine field. The derivatives... 

Tests on pig gut contents using molecular probes to detect the presence of (aerobic) ammonia oxidizers proved negative. Recently, the anaerobic oxidation of ammonia coupled to nitrate reduction has been demonstrated in... 

Field effects can be determined by calculating the effect of a bond dipole on a molecular probe at a specifted distance. One system that has been examined is H2 aligned with an H—X molecule. The substituent effect is related to the charge which develops at Ha, relative to the case where X = H. 

The orthogonally-protected Cys moiety thus serves as a convenient handle that can be used to link aPNA modules together in order to expand its nucleic acid binding capability and/or attach molecular probes. 

Over 40 different types of polypeptide toxins have been found in marine animals (i). Many of these toxins are exquisitely selective in their actions, affecting a single process or receptor at minute concentrations. So far the sea anemone and gastropod Conus) toxins have attracted the most attention as molecular probes of ion channels. In this chapter, we discuss several approaches which are being used to investigate, at the molecular level, the interactions of the sea anemone neurotoxic polypeptides with sodium channels. 

Figure 23. Schematic drawing that shows adamantane as a molecular probe with three fluorophore groups (FI) and a targeting part (TG) for specific molecular recognition. Taken from Ref. [112] with permission.

While our discussion will mainly focus on sifica, other oxide materials can also be used, and they need to be characterized with the same rigorous approach. For example, in the case of meso- and microporous materials such as zeolites, SBA-15, or MCM materials, the pore size, pore distribution, surface composition, and the inner and outer surface areas need to be measured since they can affect the grafting step (and the chemistry thereafter) [5-7]. Some oxides such as alumina or silica-alumina contain Lewis acid centres/sites, which can also participate in the reactivity of the support and the grafted species. These sites need to be characterized and quantified this is typically carried out by using molecular probes (Lewis bases) such as pyridine [8,9],... 

Bonfante et al. (73) used monoclonal antibodies and enzyme-gold complexes to reveal pectins and cellulose at the interface between the fungal wall and the host plasma membrane in AM roots (Fig. 6), and additional wall components have been investigated with other molecular probes (74-76). These studies indicate that the interface is an apoplastic space of high molecular complexity where the boundaries of the partners are defined. The examination of other endomycorrhizal systems has demonstrated that their interface is morphologically similar but different in composition. Cellulose and pectins are present at the interface... 

Others Molecular probes— stain all, vital stain Vital stains particularly useful for total viable cell counts 122... 

R. P. Haughland. Handbook of Fluorescent Probes and Research Chemicals, 5th ed.. Molecular Probes, Eugene, Oregon, 1994. 

If the center of mass of the molecular probe coincides with the Mossbauer nucleus, then the low-energy part of the spectrum monitors exclusively translational modes of the probe molecule thus providing a selective probe for fast translational processes on the lengthscale of several molecular diameters and larger. If, however, the center of mass does not coincide with the Mossbauer nucleus, then hindered rotations, i.e., librations, will contribute to the low-energy DOS. If... 

Liquid Membrane Ion-Selective Electrodes Response Mechanisms Studied by Optical Second Harmonic Generation and Photoswitchable lonophores as a Molecular Probe... 

IV. MOLECULAR PROBE FOR ISE MEMBRANE POTENTIALS BASED ON PHOTOSWITCHABLE AZOBIS(BENZO-15-CROWN-5) lONOPHORES [17]... 

If the photoequilibrium concentrations of the cis and trans isomers of the photoswitchable ionophore in the membrane bulk and their complexation stability constants for primary cations are known, the photoinduced change in the concentration of the complex cation in the membrane bulk can be estimated. If the same amount of change is assumed to occur for the concentration of the complex cation at the very surface of the membrane, the photoinduced change in the phase boundary potential may be correlated quantitatively to the amount of the primary cation permeated to or released from the membrane side of the interface under otherwise identical conditions. In such a manner, this type of photoswitchable ionophore may serve as a molecular probe to quantitatively correlate between the photoinduced changes in the phase boundary potential and the number of the primary cations permselectively extracted into the membrane side of the interface. Highly lipophilic derivatives of azobis(benzo-15-crown-5), 1 and 2, as well as reference compound 3 were used for this purpose (see Fig. 9 for the structures) [43]. Compared to azobenzene-modified crown ethers reported earlier [39 2], more distinct structural difference between the cis... 

Guo LD, Santschi PH (1996) A critical evaluation of the cross-flow ultrafiltration technique for sampling colloidal organic carbon in seawater. Marine Chem 55 113-127 Guo LD, Wen LS, Tang DG, Santschi PH (2000) Re-examination of cross-flow ultrafiltration for sampling aquatic colloids evidence from molecular probes. Marine Chem 69 75-90 Guo LD, Hunt BJ, Santschi PH (2001) Ultrafiltration behavior of major ions (Na, Ca, Mg, F, Cl, and SO4) in natnral waters. Water Res 35 1500-1508... 

DUAL OUTPUT MOLECULAR PROBE FOR ENZYMATIC ACTIVITY... 

A molecular probe with dual output signals offers two detection modes allowing use of the same probe in different environments. We have demonstrated how an AB2 self-immolative dendron with double quinone methide release mechanism can be applied to create a molecular probe with UV-Vis and fluorescence modes for the detection of a specific catalytic activity.15 The molecular probe is illustrated in Fig. 5.36. The central unit of the probe (the molecular adaptor) is linked to an enzymatic substrate that acts as a trigger and to two different reporter molecules. Cleavage of the enzymatic substrate triggers the release of the two reporters and a consequent activation of their signals. 

The disassembly pathway of molecular probe 39 is initiated by catalytic cleavage of phenylacetic acid by PGA, elimination of azaquinone methide, decarboxylation, and cyclization to release dimethylurea derivative and phenol 40 (Fig. 5.38). The latter rapidly undergoes double quinone methide elimination to release the two reporter units and by-product 41. The output of these cascade... 

FIGURE 5.36 A graphical illustration of a molecular probe for detection of enzymatic activity with dual output. (See the color version of this hgure in Color Plates section.)... 

FIGURE 5.37 Chemical structure of a molecular probe with UV-Vis and fluorescence outputs for penicillin G amidase activity. The phenylacetamide group (red) is a substrate for PGA. The reporter units, 4-nitrophenol and 6-aminoquinoline, provide a visible signal and a fluorescence signal, respectively, upon release. (See the color version of this figure in Color Plates section.)... 

As far as we know, this is the first molecular probe that includes two different types of reporter units activated upon on a specific stimulus. The other option to achieve dual detection would be to use two separate probes. However, in this case there could be a problem of competitive catalysis (circumstances in which the Km of the two substrate is not identical). In our probe, 6-aminoquinoline and 4-nitrophenol, detected by fluorescence and absorbance spectroscopy, respectively, were used as reporter units. Due to the synthetic flexibility of our approach, other reporter molecules with different types of functional groups, like amine or hydroxyl, can be linked to our molecular probe. The two assays must be orthogonal to each other, in order to prevent disturbances in the detection measurement. Another advantage of the probe is the aqueous solubility... 

Danieli, E. Shabat, D. Molecular probe for enzymatic activity with dual output. Bioorg. Med. Chem. 2007, 15, 7318-7324. 

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