Solvent probe

Lian T, Locke B, Kholodenko Y and Hochstrasser R M 1994 Energy flow from solute to solvent probed by femtosecond IR spectroscopy malachite green and heme protein solutions J. Rhys. 

Various modifications of the Stokes-Einstein relation have been proposed to take into account the microscopic effects (shape, free volume, solvent-probe interactions, etc.). In particular, the diffusion of molecular probes being more rapid than predicted by the theory, the slip boundary condition can be introduced, and sometimes a mixture of stick and slip boundary conditions is assumed. Equation (8.3) can then be rewritten as... 

The surface traced out by the center of a solvent probe molecule as it is rolled over the surface of a protein whose three-dimensional structure has been determined at the atomic level. Solvent-accessible surface areas can be calculated by various computer algorithms, and differences in solvent-accessible areas can be used to characterize the energetics of surface hydration as a function of changes in protein conformation, oligomerization, and complexation. 

The ciystal habit of sucrose and adipic add crystals were calculated from their intern structure and from the attachment energies of the various crystal faces. As a first attempt to indude the role of the solvent on the crystal habit, the solvent accessible areas of the faces of sucrose and adipic add and were calculated for spherical solvent probes of difierent sizes. In the sucrose system the results show that this type of calculation can qualitatively account for differences in solvent (water) adsorption hence fast growing and slow growing faces. In the adipic add system results show the presence of solvent sized receptacles that might enhance solvent interadions on various fares. The quantitative use of this type of data in crystal shape calculations could prove to be a reasonable method for incorporation of solvent effeds on calculated crystal shapes. 

Frequently, the general nature or detailed structure of an intermediate is inferred from reaction products. Radical ions are invoked in reactions between electron donors and acceptors in polar solvents. Probing the fate of chirality, stereochemistry, or an isotopic label or substituent in the products of a chemical transformation exemphfies the classical approach to mechanism. Of course, this approach is not without shortcomings. 

Another factor that contributes to the decoupling is the two particle direct correlation function. The product cn q)F q, t) defines the modified structure of the solvent probed by the solute. The value of the direct correlation function is less for smaller solutes at all wavevectors. The smaller the value of the two-particle direct correlation function, the lesser will be the contribution of the density mode to the total friction. 

A. van Hoek, and D. N. Reinhoudt, Flexibility of enzymes suspended in organic solvents probed by time-resolved fluorescence anisotropy. Evidence that enzyme activity and enantioselectidty are directly related to enzyme flexibility,... 

Figure 1.2 Definitions of cavities based on interlocking spheres. In black (dashed) the spheres centred on atoms A and B, in red the SAS, in cyan the shared parts of VWS and SES. In green the concave part of SES. In blue the crevice part of VWS. In black (dotted) some positions of tangent solvent probes (see Colour Plate section).

The reliability and sensitivity of the probe method has been emphasised. It circumvents almost completely the perturbations inherent to some other probe techniques (electron spin resonance, fluorescence). In particular, free chains appear to be ideal, non-perturbative NMR probes for testing chain segment orientation in strained rubbers. The solvent probe method is easy to handle and unexpensive, since it does not require the synthesis of... 

When studying polymer mixtures one needs to prepare packed columns containing an inert support coated with each of the base polymers and with the mixture, which therefore must be capable of being evaporated onto the support from a common solvent. Using a solvent probe one can then measure the specific retention volumes of the solvents when passed as vapour through the columns, i.e. V , V and V ... 

Model for predicting lipophilicity of compounds based on the -> solvent-accessible surface area SASA generated by a solvent probe of radius 1.4 A and a set of parameters encoding hydrophilic effects of polar groups [Iwaseef al., 1985] ... 

Broos J, Bisser AJW, Engbersen JI, Verboom W, van Hoek A, and Reinhoudt DN. Flexibility of Enzymes Suspended in Organic Solvents Probed by Time-Resolved Fluorescence Anisotropy. Evidence that Enzyme Activity and Enan-tioselectivity are Directly Related to Enzyme Flexibility. / Am Chem Soc 1995 117 12657-12663. 

Connolly surface The Connolly surface is the molecular surface related to the solvent accessible surface area but traced by the inward-facing part of a solvent probe model, represented by a sphere with a given radius, free to touch but not to penetrate the solute when the probe is rolled over its van der Waals surface. The surface combines the contact surface of a solute atom and the probe and the reentrant surface when the probe is in contact with more than one atom. 

Correlations between Z, E- and Y (Figs. 20 and 21) indicate that these parameters are useful solvent probes and it is probably better to use Z or E- as these are more easily obtained. 

The rolling sphere algorithm of Lee and Richards (1971) and a number of related algorithms yield the solvent accessible surface areas (Fig. 1). The radius of the solvent probe is near 1.5 A for water. The interface area B is the area of the protein surface that becomes buried at the interface when the two molecules associate, but, as the calculation uses only coordinates of the complex, it ignores conformation changes which may affect the accessible surface area of the components. The contribution of each molecule to B can be evaluated separately and is approximately equal to fr/2. Thus, other authors may prefer to quote values of fr/2 (Jones and Thornton, 1995, 1996). However, when the surfaces in contact have a strong curvature, the convex side tends to contribute more interface area than the concave side because accessible surface areas are measured one probe radius away from... 

Fig. 1. Accessible surface and interface in macromolecular complexes. Positions of the center of the solvent probe W define the solvent accessible surface (shaded) of molecules 1 and 2. When they form a complex, W is expelled from the interface and some of the accessible surfece is lost. The area of the buried surface is the sum of the accessible surface areas of the two molecules less that of the complex.

It should be noted that many of the scales whose use is reported below are based on the effect of the ionic liquids on a single probe molecule. While the response of the probe to the solvent in which it is dissolved is determined by all possible solvent-probe interactions, there is no reason for there to be an equal contribution from all of them for all of probes. Hence, it is important to be as aware as possible of which interactions are likely to have a strong effect on the particular probe used and which have a lesser effect. Since ionic liquids are composed of both anions and cations, either of which may preferentially solvate a particular probe molecule, this problem will be even greater than is usually the case in molecular solvents. It is probably foolhardy to take a scale generated by any one probe as a measure of what is generally understood by the term polarity. However, very useful information can still be gleaned from these studies. 

Because of their sensitivities to environmental changes, wide applications for solvatochromic compounds were found in the study of solute-solvent interactions, mainly in the characterization of bulk or microenvironments. Various polarity scales employing solvatochromic dyes as solvent probes were proposed. Because these empirical scales may be used to characterize any solvent or solvent mixture, solvatochromism played an important role in the study of a wide variety of solvent-dependent processes. 

Figure 6 The potential of mean force for two oppositely charged monovalent ions as obtained from Poisson s equation with a solvent dielectric of 78.54 and a solute dielectric of 1.0. The black line is the Coulomb s law interaction potential in a medium of constant solvent dielectric. The line with data points depicts the energies obtained from numerical solutions of Poisson s equation. The spheres depict the relative separation of the ions (large spheres) with respect to a model solvent molecule (small sphere) note the increase in energy as the separation falls below the size of the solvent probe.

The determination of properties of unknown system requires that master eurve be construeted. This master eurve is determined by testing a series of different polymers exposed to a seleeted solvent. An example of sueh a relationship is given in Figure 10.1.1. The enthalpy change caused by the acid-base adduct formation is obtained from a study of the same solid with different solvent probes (see Figure 10.1.2). Having this data, coefficients E and C can be calculated from the chemical shifts in any system. 

All probes that meet the previous requirements are not necessarily good solvent probes, however in fact, the sensitivity of the probe may be the result of various types of interaction with the solvent and the results difficult to generalize as a consequence. A probe suitable for determining a solvent effect such as polarity, acidity or basicity should be highly sensitive to the interaction concerned but scarcely responsive to other interactions so that any unwanted contributions will be negligible. However, eonstrueting a pure solvent scale also entails offsetting these side effects, which, as shown later on, raises die need to use a homomorph of the probe. 

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