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Conformational freedom

Ihe allure of methods for calculating free energies and their associated thermod)mai values such as equilibrium constants has resulted in considerable interest in free ene calculations. A number of decisions must be made about the way that the calculatior performed. One obvious choice concerns the simulation method. In principle, eit Monte Carlo or molecular dynamics can be used in practice, molecular dynamics almost always used for systems where there is a significant degree of conformatio flexibility, whereas Monte Carlo can give very good results for small molecules which either rigid or have limited conformational freedom. [Pg.593]

Cyclodextrins are macrocyclic compounds comprised of D-glucose bonded through 1,4-a-linkages and produced enzymatically from starch. The greek letter which proceeds the name indicates the number of glucose units incorporated in the CD (eg, a = 6, /5 = 7, 7 = 8, etc). Cyclodextrins are toroidal shaped molecules with a relatively hydrophobic internal cavity (Fig. 6). The exterior is relatively hydrophilic because of the presence of the primary and secondary hydroxyls. The primary C-6 hydroxyls are free to rotate and can partially block the CD cavity from one end. The mouth of the opposite end of the CD cavity is encircled by the C-2 and C-3 secondary hydroxyls. The restricted conformational freedom and orientation of these secondary hydroxyls is thought to be responsible for the chiral recognition inherent in these molecules (77). [Pg.64]

Glycine residues have more conformational freedom than any other amino acid, as discussed in Chapter 1. A glycine residue at a specific position in a protein has usually only one conformation in a folded structure but can have many different conformations in different unfolded structures of the same protein and thereby contribute to the diversity of unfolded conformations. Proline residues, on the other hand, have less conformational freedom in unfolded structures than any other residue since the proline side chain is fixed by an extra covalent bond to the main chain. Another way to decrease the number of possible unfolded structures of a protein, and hence stabilize the native structure, is, therefore, to mutate glycine residues to any other residue and to increase the number of proline residues. Such mutations can only be made at positions that neither change the conformation of the main chain in the folded structure nor introduce unfavorable, or cause the loss of favorable, contacts with neighboring side chains. [Pg.356]

Increase in conformational freedom of the hydrophobic core at temperatures below 29°C occurs [143]... [Pg.368]

Figure 1C. illustrates two conformations of a flexible polymer chain with one end fixed inside the cavity. Even with one end fixed, the chain still can assume a large number of conformations. The presence of the cavity wall, however, does exclude some conformations, for example, the dashed one shown in the sketch. This restraint of conformational freedom causes a decrease in both the entropy and the solute concentration inside the cavity. For this case it has been shown that QJ... [Pg.201]

Another idea developed by Yus et al. was to use other linkers with a low conformational freedom, such as 1,2-cyclohexanediamine derivatives. " ... [Pg.165]

The detection of the structural effects of B—C rr-bonding in unsaturated open-chain organoboranes should prove more difficult than in boracyclo-polyenes for several reasons. First, as already mentioned, there is the conformational freedom of the open-chain boranes, which reduces B(2pz)—C(2pz) overlap (cf. 17 vs. 19). Second, there is the linear overlap of 34 versus the cyclic, Htickel aromatic overlap of 35. [Pg.365]

The characteristic feature of a macromolecule in solution is its high degree of conformational freedom. The simplest possible model for an isolated macromolecule is the random walk (or... [Pg.5]

Because the 3D-structure of the receptor was not yet known, we wanted to derive a pharmacophore model, to prove this hypothesis. Most of the H2-antagonists have much conformational freedom. Evaluation of available crystal data and a systematic conformational search revealed mainly bent conformations,... [Pg.266]


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See also in sourсe #XX -- [ Pg.480 ]

See also in sourсe #XX -- [ Pg.32 ]




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