Rotation single bond

In Fig. 4-11, two different samples are displayed in their original conformations and conformations fitted to the query as they are highlighted by the CFS search process. The CFS process rotates single bonds between two atoms to find the maximum and minimum difference possible with the distance and angle constraints. Then, using a torsional fitter, it attempts to minimize in those conformations the deviations between measured values of 3D constraints and the values that are specified in the 3D-search query. 

Water accessible surface area of all atoms with negative partial charge Water accessible surface area of all atoms with positive partial charge Total charge of the molecule Number of rotatable single bonds Log of the octanol/water partition coefficient... 

In succinyl derivatives, the freely rotating single bond between carbon 2 and 3 allows the terminal carboxyl group to assume many more orientations and as a result this drastically reduces the probability that it will stay in the proper conformation long enough for deacylation to occur. Kirby et al. (46) proposed an intramolecular catalysis of amide bond hydrolysis by a proton transfer from external general acids and also showed that in dilute acid the O-protonated amide is the reactive species that initiates the deacylation process (see Reaction 3). 

Equation (8.8) confirms the strong dependency of %oPPB on both log P and TPSA surprisingly, it shows an inverse relationship between %oPPB and RTB, the number of non-terminal rotatable (single) bonds. 

The four arsenic-sulfur bonds present in the FlAsH-tetracysteine complex rigidly lock the fluorophore to the peptide so that any rotational motion reflects that of the peptide or protein rather than the dye. This is in direct contrast to conventional coupling chemistries used to modify proteins in which the fluorophore is attached by a rotatable single bond to the flexible side chain of an amino acid. 

Owing to the complexity and variety of multicyclic structures, a systematic method is needed for the evaluation of the statistical factors and ap. A practical way to evaluate statistical factors in difficult cases stems from the consideration that they coincide with the product of the symmetry numbers of reactants or products each raised to the corresponding stoichiometric coefficient [95]. The symmetry number of a molecule is defined as the total number of independent permutations of identical atoms or groups in a molecule that can be arrived at by simple rotations of the entire molecule, or by rotations about freely rotating single bonds within the molecule [96]. In practice. 

Fig. 4.1. Three chiral compounds whose stereoisomerism cannot be described in terms of stereocenters, stereogenic double bonds, or rotatable single bonds.

Both kinds of programs will miss any stereoisomers whose existence cannot formally be traced to the presence of stereocenters or stereogenic double bonds or to rotation about rotatable single bonds. Thus, the chiraUty and therefore the existence of enantiomers for e.g. [2,2]paracyclophanecarboxylic acid A, 1,12-dimethyl-benzo[c]phenanthrene B, and ( [-cyclooctene C (Figure 4.1), as well as for chiral fullerenes such as C76 cannot be detected by any of the current programs due to then-conceptual limitations. 

The following tests do not influence examples 4.2a or 4.2b. However, they allow further reductions in the number of candidates for example 4.2c. We can restrict the orientations around a rotatable single bond. Consider the situation shown in Figure 4.5b. The following should be commonly accepted ... 

---