Probe molecule structures

Table 4.1 Overview of all the probe molecule structures, their van der Waals structures in the cis and trans isomeric form and their isomerization volume... 

Another promising extension uses x-rays to probe the structure of confined molecules [72]. 

To find the most efficient selectors in the library, blue and red dye-labeled enantiomeric probe molecules 6 and 7 were prepared by linking pentafluorophenyl esters of L- and D-proline with Disperse Blue 3 and Disperse Red 1, respectively, through an isophthaloyl (shown in structures 6 and 7) or a succinyl moiety. Eor detection, a... 

The probe molecules of greatest historical interest in catalysis are the Hammett indicators [13]. The difficulty of making reliable visual or spectrophotometric observations of the state of protonation of these species on solids is well known. We have recently carried out the first NMR studies of Hanunett indicators on solid acids [ 14]. This was also the occasion of the first detailed collaboration between the authors of this article, and theoretical methods proved to strongly compliment the NMR experiments. The Hanunett story is told after first reviewing the application of theoretical chemistry to such problems. Central to the application of any physical method in chemistry is the process of modeling the relationship between the observables and molecular structure. However often one does this, it is rarely an exact process. One can rationalize almost any trend in isotropic chemical shift as a function of some variation in molecular structure - after the fact, but the quantitative prediction of such trends in advance defies intuition in most nontrivial cases. Even though the NMR spectrum is a function... 

Perturbation of structural, vibrational, and electronic features of the catalytic center by interaction with probe molecules is the most important experimental approach for understanding the accessibiUty and the reactivity of the site itself. The understanding of the system increases enormously if the experimental results are interpreted on the basis of accurate ab initio modeling. These general statements of course also hold for TS-1 [49,52,64,74-77]. Unfortunately, we do not have the space to enter into a discussion of the abim-dant computational literature published so far on TS-1 catalyst in particular and on titanoshlcates in general. The reader can find an excellent starting point in the Uterature quoted in [49,52,64,74-77,88]. 

Rousseau, R., Dietrich, G., Kruckeberg, S., Lutzenkirchen, K., Marx, D., Schweikhard, L. and Walther, C. (1998) Probing cluster structures with sensor molecules methanol adsorbed onto gold clusters. Chemical Physics Letters, 295, 41-46. 

FIG. 2 Structures of the probe molecules used iu the studies reviewed. 

Eisenthal and coworkers have also measured interfacial friction via the rotational dynamics of probe molecules at the interface. In their first study, Eisenthal and coworkers probed the rotational dynamics of rhodamine 6G (R6G, structure shown in Fig. 2) at the... 

The probing of the active site of an enzyme by using multiple crystal structures containing different small molecules was originally described using different organic solvents as the probe molecules [21]. This technique showed how the information derived from the small molecules binding in... 

NMR Self-Diffusion of Desmopressin. The NMR-diffusion technique (3,10) offers a convenient way to measure the translational self-diffusion coefficient of molecules in solution and in isotropic liquid crystalline phases. The technique is nonperturbing, in that it does not require the addition of foreign probe molecules or the creation of a concentration-gradient in the sample it is direct in that it does not involve any model dependent assumptions. Obstruction by objects much smaller than the molecular root-mean-square displacement during A (approx 1 pm), lead to a reduced apparent diffusion coefficient in equation (1) (10). Thus, the NMR-diffusion technique offers a fruitful way to study molecular interactions in liquids (11) and the phase structure of liquid crystalline phases (11,12). 

Most of the molecules introduced in this chapter are hydrophobic. Even those molecules that have been functionalized to improve water-solubility (for example, CCVJ and CCVJ triethyleneglycol ester 43, Fig. 14) contain large hydrophobic structures. In aqueous solutions that contain proteins or other macromolecules with hydrophobic regions, molecular rotors are attracted to these pockets and bind to the proteins. Noncovalent attraction to hydrophobic pockets is associated with restricted intramolecular rotation and consequently increased quantum yield. In this respect, molecular rotors are superior protein probes, because they do not only indicate the presence of proteins (similar to antibody-conjugated fluorescent markers), but they also report a constricted environment and can therefore be used to probe protein structure and assembly. 

Perrin et al. probed the structures of 174 and 175 by using the 13C NMR method of isotopic perturbation of equilibrium <2001PCA11383>. The goal of this study was to measure the 13C NMR chemical-shift difference between C5 of a-deuterated molecule and C2-(5) of undeuterated molecule (see Equation 48). If 174 or 175 is a mixture of valence tautomers 180-r/ia and 180-r/]b or 181-equilibrium isotope shift (Aeq) will be observed in addition to the intrinsic isotope shift (5A0). In contrast, if 174 or 175 has C2v symmetry, then only (5A0) will contribute. 

The aluminum is incorporated in a tetrahedral way into the mesoporous structure, given place to Bronsted acidic sites which are corroborated by FTIR using pyridine as probe molecule. The presence of aluminum reduces the quantity of amorphous carbon produced in the synthesis of carbon nanotubes which does not happen for mesoporous silica impregnated only with iron. It was observed a decrease in thermal stability of MWCNTs due to the presence of more metal particles which help to their earlier oxidation process. 

In view of catalytic potential applications, there is a need for a convenient means of characterization of the porosity of new catalyst materials in order to quickly target the potential industrial catalytic applications of the studied catalysts. The use of model test reactions is a characterization tool of first choice, since this method has been very successful with zeolites where it precisely reflects shape-selectivity effects imposed by the porous structure of tested materials. Adsorption of probe molecules is another attractive approach. Both types of approaches will be presented in this work. The methodology developed in this work on zeolites Beta, USY and silica-alumina may be appropriate for determination of accessible mesoporosity in other types of dealuminated zeolites as well as in hierarchical materials presenting combinations of various types of pores. 

The physical properties of probe molecules adsorbed in the confined space of porous materials are known to vary in dependence of structural constraints on molecular motion. Detailed investigations of adsorption geometries are possible, when well-defined sites and loadings exist. This was the case for the adsorption of strongly interacting probe molecules, such as pyridine, on SiOH groups in the... 

A remarkable application of phosphines by Grey and coworkers for acid site characterization is the use of diphosphines with alkyl chain spacers of different length between the phosphine moieties. Based on careful NMR analysis and appropriate loading levels with diphosphines, the Al distribution can be determined [223, 224], The idea behind this tool is that the phosphine groups will be proto-nated, when they are close to an acid site in the zeolite structure. Protonation of both phosphine groups in one probe molecule will only occur, when the distance between the two acid sites is compatible with the molecular dimension of the diphosphine. 

The analysis of the structural properties of zeolitic acid sites based on dipolar interactions has further improved the understanding of acidity. Grey and Vega were the first to apply the 1H 27A1 TRAPDOR technique [36]. The REAPDOR method was first applied by Kalwei and coauthors [236-238] on bare acid sites and also on zeolites loaded with probe molecules. These methods allow one to distinguish... 

The previous result is an important one. It indicates that there can be yet another fruitful route to describe lipid bilayers. The idea is to consider the conformational properties of a probe molecule, and then replace all the other molecules by an external potential field (see Figure 11). This external potential may be called the mean-field or self-consistent potential, as it represents the mean behaviour of all molecules self-consistently. There are mean-field theories in many branches of science, for example (quantum) physics, physical chemistry, etc. Very often mean-field theories simplify the system to such an extent that structural as well as thermodynamic properties can be found analytically. This means that there is no need to use a computer. However, the lipid membrane problem is so complicated that the help of the computer is still needed. The method has been refined over the years to a detailed and complex framework, whose results correspond closely with those of MD simulations. The computer time needed for these calculations is however an order of 105 times less (this estimate is certainly too small when SCF calculations are compared with massive MD simulations in which up to 1000 lipids are considered). Indeed, the calculations can be done on a desktop PC with typical... 

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