Anisotropic environments

Conversely, in a membrane model, acetylcholine showed mean log P values very similar to those exhibited in water. This was due to the compound remaining in the vicinity of the polar phospholipid heads, but the disappearance of extended forms decreased the average log P value somewhat. This suggests that an anisotropic environment can heavily modify the conformational profile of a solute, thus selecting the conformational clusters more suitable for optimal interactions. In other words, isotropic media select the conformers, whereas anisotropic media select the conformational clusters. The difference in conformational behavior in isotropic versus anisotropic environments can be explained considering that the physicochemical effects induced by an isotropic medium are homogeneously uniform around the solute so that all conformers are equally influenced by them. In contrast, the physicochemical effects induced by an anisotropic medium are not homogeneously distributed and only some conformational clusters can adapt to them. 

Although continuum solvation models do appear to reproduce the structural and spectroscopic properties of many molecules in solution, parameterization remains an issue in studies involving solvents other than water. In addition, the extension of these approaches to study proteins embedded in anisotropic environments, such as cell membranes, is clearly a difficult undertaking96. As a result, several theoretical studies have been undertaken to develop semi-empirical methods that can calculate the electronic properties of very large systems, such as proteins28,97 98. The principal problem in describing systems comprised of many basis functions is the method for solving the semi-empirical SCF equations ... 

Calculations of forces may be improved in several ways. One is to pursue efforts towards the development of accurate classical, atomic-level force fields. A promising extension along these lines is to add nonadditive polarization effects to the usual pairwise additive description of interatomic interactions. This has been attempted in the past [35-39], but has not brought the expected and long-awaited improvements. This is not so much because polarization effects are not important, or pairwise additive models can account for them accurately in an average sense in all, even highly anisotropic environments. Instead, it seems more likely that the previously developed nonadditive potentials were not sufficiently accurate to offer an enhanced description of those systems in which induction phenomena play a crucial role. 

This section recalls several physical elements of mechanical wave propagation. It is by no way exhaustive and more detailed information can be found in Refs. 18-21. Moreover this theoretical part will be restricted to linear acoustics, first described in simple media and then extended to more complicated viscous anisotropic environments. 

In a multidomain protein whose domains have fixed orientations relative to each other, a unique alignment tensor will represent the preferred orientation of all the domains in the anisotropic environment. Therefore, structure refinement with dipolar couplings is performed as in one-domain proteins (Sect. 8.4). Several examples are reported in the literature of cases with conformational ambiguity due to the lack of NOE contacts between the domains. One example is the determination of subdomain orientation of the riboso-mal protein S4 z)41 [97]. In this work the lack of NOE contacts between the domains produces an ambiguity in interdomain orientation. The authors use two different anisotropic media to obtain dipolar couplings (DMPC/DHPC bicelles and Pfl filamentous bacteriophages). They conclude that subdomain orientation in solution is similar to the one present in the crystal structure. 

All these deviations have one similarity they occur in compounds having relatively crowded chiral centers bearing at least one highly anisotropic substituent. The differential effect of the CSA on the intramolecular anisotropic environment of a given nucleus (e.g., on aryl rotation) cannot presently be stated. 

Silica gel surfaces (Figure 9) offer an anisotropic environment to adsorbed ketone molecules in which motions are restricted (in a crude sense) to two dimensions. Under the best of circumstances, a distribution of site sizes and... 

The last decade or so has witnessed a great deal of activity to explore the influences of anisotropic environments on photochemical reactions. Results from this research have led to a rudimentary understanding of how photochemical processes may be directed by media in individual cases, but... 

As well as providing a means of measuring 1 H/2H-exchange in proteins, NMR is a most powerful technique for studying the mobility of individual amino acids. For example, the rotational freedom of the aromatic side chains of tyrosine and phenylalanine about the C 3—Cy bond is readily studied by various NMR methods. ]H NMR can detect whether or not the aromatic ring is constrained in an anisotropic environment. In an isotropic environment or where there is rapid rotation on the NMR time scale, the 3 and 5 protons of phenylalanine and tyrosine are symmetrically related, as are the 2 and 6 (structures 1.12). The resultant spectrum is of the AA BB type, containing two pairs of closely separated doublets. But if there is slow rotation in an anisotropic environment, the symmetry breaks down to give four separate resonances (an ABCD spectrum), since the 5 and 6 protons are in different states from the 2 and 3. At an intermediate time... 

Similarly, the reaction field, R (88-90), associated with a group of solvent molecules with cholesteric phase order is much larger when operating on a triplet of BN R increases with increasing a. Hie limitations of the Onsager model to the very anisotropic environment experienced by 2BN preclude a reasonable quantitative discussion. The solute cavity Is not spherical BN may be described better for the purposes of elucidating its interactions with neighboring solvent molecules as a quadrupole... 

Adsorption chromatography is based on competition for neutral analytes between the liquid mobile phase and a neutral, solid stationary phase. The analytes interact with the stationary phase according to the premise like likes like polar solutes will be retained longest by polar stationary phases, and nonpolar solutes will be retained best by nonpolar stationary phases. In adsorption chromatography the solute molecules are in contact with both the stationary phase and the mobile phase, simultaneously. Under these conditions, the solutes are said to be in an anisotropic environment. 

Let us note that one can neglect the effect of anisotropic environment and have obtained the simpler linear form of relaxation equation... 

At small gradients, the right parts of these relations can be expanded in a power series. In linear approximation of a parity for the anisotropic environment one gets... 

Because quadrupolar nuclides have I > /2, there are more energy levels to consider, and the probability of a relaxation transition between one pair of levels in a single nucleus may not be equal to that between another pair of levels. For example, nuclides with I = 3/2 (such as 23Na) have distinctly different relaxation rates for the m — % — V2 transition and the V2 — 3/2 transitions. In an even slightly anisotropic environment, such as a liquid crystal solvent or a biological cell, the spectrum of a free 23Na ion has two components, as indicated in Fig. 8.5, with quite different values of both T, and T2. 

The most important difference between particles inside the bulk and in the interfacial layer comes from the surrounding environment of the particles the particles inside the bulk are in an isotropic environment, while those in the interface are in an anisotropic environment thus, in the interlayer, the forces between the particles are unbalanced. To reduce the resulting surface pressure, some additional processes occur that must be taken into account. On clean surfaces (for example, on a solid surface in vacuum), these processes are the bond-length contraction or relaxation and reconstruction of the surface particles (Somorjai 1994). It results in significantly reduced spacing between the first and second layers compared to the bulk. The perturbation caused by this movement propagates a few layers into the bulk. The other effect is that the equilibrium position of the particles changes that is the outermost layers can have different crystal structure than the bulk. This phenomenon is the reconstruction. 

The catalytic sites of most enzymes are not exposed to the bulk water phase. Thus, substrates fixed at a catalytic site are found in an extremely anisotropic environment, which is impossible to attain in homogeneous... 

R288 L. Cristofolini and M. P. Fontana, Vibrational Properties and Phase Transitions in Lithium Doped Fullerides , Asian J. Phys., 2000,9, 609 R289 T. A. Cross and J. R. Quine, Protein Structure in Anisotropic Environments Development of Orientational Constraints , Concepts Magn. Reson., 2000,12, 55... 

A molecular dynamics simulation has been performed on 4-n-pentyl-4(-cyanobiphenyl (5CB) in the nematic phase. Order parameters and dipolar couplings have been calculated and used to test theoretical models. Theoretical models have also been developed to explain the shielding of a noble-gas atom in an anisotropic environment and applied to explain the medium-induced shielding of the noble gases Xe and Ne in the nematic liquid crystal 4(-ethoxybenzylidene-4-n-butylaniline (EBBA). ... 

Therefore, on multiple fronts the prospects for N solid-state NMR are promising. In the past couple of years, high resolution 3D polypeptide structure has been obtained from samples in anisotropic environments where structures are unobtainable by other means. Recently, new methods have been developed that will permit the observation of uniformly labeled samples. The coupling of distance and orientational constraints will be an exceptionally powerful structural approach. While the methods have been primarily demonstrated here with polypeptides and proteins, studies of nucleic acids and... 

Isotropic ESR spectra, sometimes exhibiting coupling to the 109Ag and 107Ag nuclear spins, are often observed at room temperature. Spectra observed at lower temperature in glasses are generally more complicated because the complexes are in an anisotropic environment (Figure 7)37. 

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